Starting phenix.real_space_refine on Fri Feb 23 20:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z87_14545/02_2024/7z87_14545_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z87_14545/02_2024/7z87_14545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z87_14545/02_2024/7z87_14545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z87_14545/02_2024/7z87_14545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z87_14545/02_2024/7z87_14545_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z87_14545/02_2024/7z87_14545_updated.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 52 5.49 5 S 235 5.16 5 Cl 1 4.86 5 C 25160 2.51 5 N 6701 2.21 5 O 7558 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A GLU 814": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A PHE 1344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1413": "OD1" <-> "OD2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A GLU 1516": "OE1" <-> "OE2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A PHE 1729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A TYR 1945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2087": "OE1" <-> "OE2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A PHE 2157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A GLU 2188": "OE1" <-> "OE2" Residue "A ARG 2214": "NH1" <-> "NH2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A ASP 2247": "OD1" <-> "OD2" Residue "A PHE 2260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2284": "OD1" <-> "OD2" Residue "A TYR 2288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A GLU 2314": "OE1" <-> "OE2" Residue "A GLU 2338": "OE1" <-> "OE2" Residue "A GLU 2357": "OE1" <-> "OE2" Residue "A ARG 2427": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A ARG 2485": "NH1" <-> "NH2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2745": "NH1" <-> "NH2" Residue "A ARG 2753": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A GLU 2819": "OE1" <-> "OE2" Residue "A ASP 2821": "OD1" <-> "OD2" Residue "A PHE 2848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2962": "NH1" <-> "NH2" Residue "A ASP 3000": "OD1" <-> "OD2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A GLU 3309": "OE1" <-> "OE2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A TYR 3334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3344": "OE1" <-> "OE2" Residue "A GLU 3429": "OE1" <-> "OE2" Residue "A ARG 3462": "NH1" <-> "NH2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A ASP 3509": "OD1" <-> "OD2" Residue "A TYR 3614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3630": "NH1" <-> "NH2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A ARG 3718": "NH1" <-> "NH2" Residue "A ARG 3733": "NH1" <-> "NH2" Residue "A ARG 3734": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A GLU 3824": "OE1" <-> "OE2" Residue "A ASP 3851": "OD1" <-> "OD2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A PHE 3904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A ARG 3965": "NH1" <-> "NH2" Residue "A PHE 4005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4125": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39708 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 29194 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3689, 29184 Classifications: {'peptide': 3689} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 3531} Chain breaks: 18 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 31, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 286 Conformer: "B" Number of residues, atoms: 3689, 29184 Classifications: {'peptide': 3689} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 3531} Chain breaks: 18 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 31, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 286 bond proxies already assigned to first conformer: 29758 Chain: "B" Number of atoms: 3953 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 490, 3937 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 490, 3937 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3996 Chain: "C" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5267 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 633} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "E" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 540 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 188 Unusual residues: {'1IX': 1} Classifications: {'undetermined': 1, 'water': 154} Link IDs: {None: 154} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A3122 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A3122 " occ=0.50 Time building chain proxies: 35.69, per 1000 atoms: 0.90 Number of scatterers: 39708 At special positions: 0 Unit cell: (126.488, 169.52, 236.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 235 16.00 P 52 15.00 F 1 9.00 O 7558 8.00 N 6701 7.00 C 25160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.89 Conformation dependent library (CDL) restraints added in 13.5 seconds 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 226 helices and 11 sheets defined 56.0% alpha, 3.8% beta 21 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 29.73 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.970A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 76 through 95 removed outlier: 4.745A pdb=" N GLU A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 Proline residue: A 102 - end of helix removed outlier: 4.804A pdb=" N VAL A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.514A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.520A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.779A pdb=" N ASN A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 356 through 376 removed outlier: 4.336A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 3.867A pdb=" N VAL A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.760A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 432 through 444 Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 473 through 491 removed outlier: 4.301A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 removed outlier: 4.708A pdb=" N ASP A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 Processing helix chain 'A' and resid 617 through 633 removed outlier: 3.929A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.555A pdb=" N VAL A 646 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 648 " --> pdb=" O TRP A 645 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 649 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 650 " --> pdb=" O TYR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 679 Processing helix chain 'A' and resid 700 through 720 removed outlier: 4.947A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 745 through 758 removed outlier: 3.894A pdb=" N VAL A 749 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Proline residue: A 750 - end of helix removed outlier: 4.222A pdb=" N GLN A 753 " --> pdb=" O PRO A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 Processing helix chain 'A' and resid 786 through 795 removed outlier: 4.672A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix Processing helix chain 'A' and resid 797 through 799 No H-bonds generated for 'chain 'A' and resid 797 through 799' Processing helix chain 'A' and resid 817 through 824 removed outlier: 3.898A pdb=" N LYS A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 838 Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 866 through 869 Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 911 through 919 Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.514A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 974 removed outlier: 3.551A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.804A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 995 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1023 through 1042 removed outlier: 3.602A pdb=" N ASP A1027 " --> pdb=" O SER A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1072 through 1085 Processing helix chain 'A' and resid 1096 through 1116 removed outlier: 5.344A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1140 removed outlier: 3.595A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1175 Processing helix chain 'A' and resid 1181 through 1194 Processing helix chain 'A' and resid 1204 through 1215 Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.972A pdb=" N ASN A1222 " --> pdb=" O PHE A1219 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A1223 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1251 through 1266 Processing helix chain 'A' and resid 1268 through 1272 Processing helix chain 'A' and resid 1278 through 1282 Processing helix chain 'A' and resid 1290 through 1300 removed outlier: 4.096A pdb=" N SER A1300 " --> pdb=" O PHE A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1350 removed outlier: 3.835A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1359 No H-bonds generated for 'chain 'A' and resid 1357 through 1359' Processing helix chain 'A' and resid 1366 through 1376 Processing helix chain 'A' and resid 1391 through 1408 Proline residue: A1396 - end of helix removed outlier: 4.263A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1422 removed outlier: 4.080A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1447 through 1461 Processing helix chain 'A' and resid 1464 through 1467 No H-bonds generated for 'chain 'A' and resid 1464 through 1467' Processing helix chain 'A' and resid 1478 through 1490 Processing helix chain 'A' and resid 1505 through 1521 removed outlier: 3.857A pdb=" N GLN A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A1511 " --> pdb=" O CYS A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1532 Processing helix chain 'A' and resid 1557 through 1562 Processing helix chain 'A' and resid 1566 through 1573 Processing helix chain 'A' and resid 1575 through 1585 removed outlier: 4.210A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1606 Processing helix chain 'A' and resid 1613 through 1628 removed outlier: 4.961A pdb=" N LYS A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS A1628 " --> pdb=" O GLN A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1655 Processing helix chain 'A' and resid 1668 through 1680 Processing helix chain 'A' and resid 1686 through 1698 removed outlier: 4.089A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A1696 " --> pdb=" O ALA A1692 " (cutoff:3.500A) Proline residue: A1697 - end of helix Processing helix chain 'A' and resid 1707 through 1718 Processing helix chain 'A' and resid 1734 through 1752 Processing helix chain 'A' and resid 1756 through 1768 removed outlier: 3.653A pdb=" N GLU A1760 " --> pdb=" O PRO A1756 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A1761 " --> pdb=" O MET A1757 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1786 Processing helix chain 'A' and resid 1791 through 1806 Processing helix chain 'A' and resid 1813 through 1830 removed outlier: 3.792A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A1830 " --> pdb=" O THR A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1851 removed outlier: 4.090A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1882 Processing helix chain 'A' and resid 1887 through 1890 No H-bonds generated for 'chain 'A' and resid 1887 through 1890' Processing helix chain 'A' and resid 1896 through 1899 No H-bonds generated for 'chain 'A' and resid 1896 through 1899' Processing helix chain 'A' and resid 1909 through 1923 removed outlier: 4.087A pdb=" N LYS A1913 " --> pdb=" O ASN A1909 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1954 removed outlier: 3.672A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1962 through 1965 No H-bonds generated for 'chain 'A' and resid 1962 through 1965' Processing helix chain 'A' and resid 1971 through 1973 No H-bonds generated for 'chain 'A' and resid 1971 through 1973' Processing helix chain 'A' and resid 1978 through 1981 No H-bonds generated for 'chain 'A' and resid 1978 through 1981' Processing helix chain 'A' and resid 2035 through 2047 Processing helix chain 'A' and resid 2094 through 2106 Processing helix chain 'A' and resid 2125 through 2133 Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2154 through 2163 Proline residue: A2159 - end of helix removed outlier: 5.247A pdb=" N LYS A2162 " --> pdb=" O ARG A2158 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N HIS A2163 " --> pdb=" O PRO A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2173 Processing helix chain 'A' and resid 2185 through 2195 Processing helix chain 'A' and resid 2206 through 2221 Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2256 through 2260 Processing helix chain 'A' and resid 2271 through 2282 Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 3.895A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 removed outlier: 4.444A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2353 removed outlier: 3.559A pdb=" N GLN A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2370 removed outlier: 4.172A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 3.558A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) Processing helix chain 'A' and resid 2379 through 2388 Proline residue: A2387 - end of helix Processing helix chain 'A' and resid 2392 through 2404 removed outlier: 3.955A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2417 Processing helix chain 'A' and resid 2420 through 2425 removed outlier: 3.525A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2445 Proline residue: A2444 - end of helix Processing helix chain 'A' and resid 2448 through 2461 removed outlier: 3.866A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 4.609A pdb=" N PHE A2461 " --> pdb=" O PRO A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2467 through 2481 Processing helix chain 'A' and resid 2495 through 2511 removed outlier: 3.592A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A2500 " --> pdb=" O GLN A2496 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE A2511 " --> pdb=" O ILE A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2517 through 2526 Processing helix chain 'A' and resid 2535 through 2545 removed outlier: 3.949A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2548 through 2563 removed outlier: 5.428A pdb=" N VAL A2552 " --> pdb=" O LYS A2549 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU A2555 " --> pdb=" O VAL A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2736 through 2766 removed outlier: 4.128A pdb=" N LYS A2762 " --> pdb=" O LYS A2758 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET A2763 " --> pdb=" O SER A2759 " (cutoff:3.500A) Processing helix chain 'A' and resid 2788 through 2798 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2802 through 2821 removed outlier: 3.873A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2826 through 2846 Processing helix chain 'A' and resid 2852 through 2863 Processing helix chain 'A' and resid 2866 through 2868 No H-bonds generated for 'chain 'A' and resid 2866 through 2868' Processing helix chain 'A' and resid 2873 through 2882 Processing helix chain 'A' and resid 2886 through 2897 Processing helix chain 'A' and resid 2920 through 2933 Processing helix chain 'A' and resid 2945 through 2947 No H-bonds generated for 'chain 'A' and resid 2945 through 2947' Processing helix chain 'A' and resid 2951 through 2961 Processing helix chain 'A' and resid 2965 through 2976 removed outlier: 3.603A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2988 through 3004 Processing helix chain 'A' and resid 3008 through 3016 Processing helix chain 'A' and resid 3034 through 3036 No H-bonds generated for 'chain 'A' and resid 3034 through 3036' Processing helix chain 'A' and resid 3041 through 3053 Processing helix chain 'A' and resid 3061 through 3068 Processing helix chain 'A' and resid 3073 through 3081 Processing helix chain 'A' and resid 3085 through 3092 Processing helix chain 'A' and resid 3096 through 3116 removed outlier: 3.583A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3125 through 3146 removed outlier: 4.268A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA A3134 " --> pdb=" O GLN A3130 " (cutoff:3.500A) Processing helix chain 'A' and resid 3155 through 3165 Processing helix chain 'A' and resid 3176 through 3195 Processing helix chain 'A' and resid 3227 through 3249 removed outlier: 3.620A pdb=" N CYS A3234 " --> pdb=" O LEU A3230 " (cutoff:3.500A) Processing helix chain 'A' and resid 3252 through 3262 Processing helix chain 'A' and resid 3270 through 3288 Processing helix chain 'A' and resid 3296 through 3307 removed outlier: 4.062A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A3304 " --> pdb=" O VAL A3300 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3343 Processing helix chain 'A' and resid 3347 through 3350 No H-bonds generated for 'chain 'A' and resid 3347 through 3350' Processing helix chain 'A' and resid 3356 through 3360 Processing helix chain 'A' and resid 3372 through 3393 Processing helix chain 'A' and resid 3410 through 3428 removed outlier: 3.739A pdb=" N PHE A3419 " --> pdb=" O THR A3415 " (cutoff:3.500A) Processing helix chain 'A' and resid 3434 through 3439 Processing helix chain 'A' and resid 3442 through 3455 removed outlier: 3.517A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3464 removed outlier: 4.168A pdb=" N LYS A3464 " --> pdb=" O GLU A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3466 through 3473 removed outlier: 4.035A pdb=" N ILE A3471 " --> pdb=" O LEU A3468 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A3472 " --> pdb=" O LEU A3469 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A3473 " --> pdb=" O GLN A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3481 through 3489 removed outlier: 3.990A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3492 through 3502 removed outlier: 3.760A pdb=" N PHE A3495 " --> pdb=" O CYS A3492 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A3497 " --> pdb=" O GLN A3494 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A3499 " --> pdb=" O ILE A3496 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3524 Processing helix chain 'A' and resid 3530 through 3539 removed outlier: 3.813A pdb=" N SER A3539 " --> pdb=" O ILE A3535 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3561 removed outlier: 3.515A pdb=" N VAL A3555 " --> pdb=" O ASN A3551 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3576 Processing helix chain 'A' and resid 3581 through 3594 Processing helix chain 'A' and resid 3605 through 3615 removed outlier: 4.138A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A3614 " --> pdb=" O TYR A3610 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3626 removed outlier: 3.749A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3633 through 3639 Processing helix chain 'A' and resid 3642 through 3649 removed outlier: 4.054A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3651 through 3653 No H-bonds generated for 'chain 'A' and resid 3651 through 3653' Processing helix chain 'A' and resid 3661 through 3672 removed outlier: 3.503A pdb=" N ASN A3671 " --> pdb=" O LEU A3667 " (cutoff:3.500A) Processing helix chain 'A' and resid 3681 through 3683 No H-bonds generated for 'chain 'A' and resid 3681 through 3683' Processing helix chain 'A' and resid 3759 through 3774 Processing helix chain 'A' and resid 3779 through 3783 Processing helix chain 'A' and resid 3812 through 3819 Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3847 removed outlier: 3.833A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3860 removed outlier: 4.005A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3877 removed outlier: 4.036A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3894 through 3917 Processing helix chain 'A' and resid 3965 through 3971 removed outlier: 3.851A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3979 through 3994 removed outlier: 4.398A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3996 through 4007 removed outlier: 3.955A pdb=" N ASP A4003 " --> pdb=" O THR A3999 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL A4004 " --> pdb=" O ASN A4000 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE A4005 " --> pdb=" O THR A4001 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A4006 " --> pdb=" O MET A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4049 removed outlier: 3.601A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4056 through 4068 Processing helix chain 'A' and resid 4074 through 4082 Processing helix chain 'A' and resid 4089 through 4091 No H-bonds generated for 'chain 'A' and resid 4089 through 4091' Processing helix chain 'A' and resid 4100 through 4111 Processing helix chain 'A' and resid 4114 through 4117 No H-bonds generated for 'chain 'A' and resid 4114 through 4117' Processing helix chain 'A' and resid 4122 through 4124 No H-bonds generated for 'chain 'A' and resid 4122 through 4124' Processing helix chain 'B' and resid 59 through 77 removed outlier: 4.244A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 removed outlier: 4.660A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.061A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 481 through 495 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.873A pdb=" N ILE C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 199 through 222 removed outlier: 8.616A pdb=" N GLU C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ASP C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.757A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 372 through 386 Processing helix chain 'C' and resid 448 through 460 Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 510 through 515 Processing helix chain 'C' and resid 520 through 536 removed outlier: 5.011A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 550 through 553 No H-bonds generated for 'chain 'C' and resid 550 through 553' Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 613 through 625 Processing helix chain 'C' and resid 629 through 648 Processing helix chain 'C' and resid 652 through 668 Processing helix chain 'C' and resid 673 through 681 Processing helix chain 'C' and resid 700 through 704 Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.632A pdb=" N LEU C 729 " --> pdb=" O VAL C 725 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 725 through 730' Processing sheet with id= A, first strand: chain 'A' and resid 893 through 895 Processing sheet with id= B, first strand: chain 'A' and resid 3747 through 3749 Processing sheet with id= C, first strand: chain 'A' and resid 3750 through 3753 removed outlier: 6.135A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id= E, first strand: chain 'B' and resid 198 through 204 removed outlier: 6.715A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 82 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE B 40 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 84 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 42 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 86 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE B 87 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL B 104 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 258 through 262 removed outlier: 7.804A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 349 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR B 401 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU B 345 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 318 through 322 Processing sheet with id= H, first strand: chain 'C' and resid 224 through 226 removed outlier: 9.393A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 9 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU C 133 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 11 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N PHE C 135 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N CYS C 13 " --> pdb=" O PHE C 135 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 257 through 264 removed outlier: 3.739A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE C 340 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 391 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 314 through 316 Processing sheet with id= K, first strand: chain 'C' and resid 464 through 466 removed outlier: 3.691A pdb=" N LYS C 465 " --> pdb=" O GLU C 474 " (cutoff:3.500A) 1737 hydrogen bonds defined for protein. 4953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 28.14 Time building geometry restraints manager: 18.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12476 1.34 - 1.46: 9104 1.46 - 1.59: 18360 1.59 - 1.71: 100 1.71 - 1.83: 374 Bond restraints: 40414 Sorted by residual: bond pdb=" C11 1IX A4201 " pdb="CL1 1IX A4201 " ideal model delta sigma weight residual 1.728 1.835 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C24 1IX A4201 " pdb=" N26 1IX A4201 " ideal model delta sigma weight residual 1.371 1.472 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C12 1IX A4201 " pdb=" C13 1IX A4201 " ideal model delta sigma weight residual 1.379 1.466 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C14 1IX A4201 " pdb=" C16 1IX A4201 " ideal model delta sigma weight residual 1.480 1.562 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C ASP B 341 " pdb=" N ASP B 342 " ideal model delta sigma weight residual 1.329 1.253 0.076 1.86e-02 2.89e+03 1.67e+01 ... (remaining 40409 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.48: 628 103.48 - 111.14: 16521 111.14 - 118.80: 16226 118.80 - 126.45: 20828 126.45 - 134.11: 638 Bond angle restraints: 54841 Sorted by residual: angle pdb=" N THR A 169 " pdb=" CA THR A 169 " pdb=" C THR A 169 " ideal model delta sigma weight residual 113.72 97.24 16.48 1.30e+00 5.92e-01 1.61e+02 angle pdb=" C MET A 948 " pdb=" N PRO A 949 " pdb=" CA PRO A 949 " ideal model delta sigma weight residual 119.84 128.86 -9.02 1.25e+00 6.40e-01 5.21e+01 angle pdb=" N ILE A2137 " pdb=" CA ILE A2137 " pdb=" C ILE A2137 " ideal model delta sigma weight residual 113.71 107.53 6.18 9.50e-01 1.11e+00 4.23e+01 angle pdb=" N LYS A 165 " pdb=" CA LYS A 165 " pdb=" C LYS A 165 " ideal model delta sigma weight residual 111.28 119.80 -8.52 1.35e+00 5.49e-01 3.98e+01 angle pdb=" C SER A2547 " pdb=" N PRO A2548 " pdb=" CA PRO A2548 " ideal model delta sigma weight residual 119.84 127.04 -7.20 1.25e+00 6.40e-01 3.32e+01 ... (remaining 54836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 23855 34.15 - 68.29: 668 68.29 - 102.44: 48 102.44 - 136.59: 1 136.59 - 170.73: 1 Dihedral angle restraints: 24573 sinusoidal: 10325 harmonic: 14248 Sorted by residual: dihedral pdb=" CA LEU A2122 " pdb=" C LEU A2122 " pdb=" N PRO A2123 " pdb=" CA PRO A2123 " ideal model delta harmonic sigma weight residual -180.00 -143.46 -36.54 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA LYS A1960 " pdb=" C LYS A1960 " pdb=" N PHE A1961 " pdb=" CA PHE A1961 " ideal model delta harmonic sigma weight residual 180.00 149.04 30.96 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA PRO A1020 " pdb=" C PRO A1020 " pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta harmonic sigma weight residual -180.00 -149.19 -30.81 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 24570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5767 0.084 - 0.168: 458 0.168 - 0.252: 15 0.252 - 0.336: 1 0.336 - 0.420: 2 Chirality restraints: 6243 Sorted by residual: chirality pdb=" CA HIS C 411 " pdb=" N HIS C 411 " pdb=" C HIS C 411 " pdb=" CB HIS C 411 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA ASP A 168 " pdb=" N ASP A 168 " pdb=" C ASP A 168 " pdb=" CB ASP A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA LYS A 165 " pdb=" N LYS A 165 " pdb=" C LYS A 165 " pdb=" CB LYS A 165 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 6240 not shown) Planarity restraints: 6791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 165 " 0.027 2.00e-02 2.50e+03 5.36e-02 2.88e+01 pdb=" C LYS A 165 " -0.093 2.00e-02 2.50e+03 pdb=" O LYS A 165 " 0.035 2.00e-02 2.50e+03 pdb=" N ILE A 166 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 499 " -0.063 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO B 500 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 166 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ILE A 166 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE A 166 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 167 " 0.019 2.00e-02 2.50e+03 ... (remaining 6788 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4723 2.74 - 3.28: 43410 3.28 - 3.82: 68307 3.82 - 4.36: 83176 4.36 - 4.90: 134608 Nonbonded interactions: 334224 Sorted by model distance: nonbonded pdb=" O PRO A3960 " pdb=" O HOH A4301 " model vdw 2.199 2.440 nonbonded pdb=" O GLY A1964 " pdb=" OG SER A1968 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP A 887 " pdb=" NH1 ARG A 891 " model vdw 2.199 2.520 nonbonded pdb=" O VAL A2938 " pdb=" O HOH A4302 " model vdw 2.204 2.440 nonbonded pdb=" NH1 ARG B 399 " pdb=" O LEU C 516 " model vdw 2.204 2.520 ... (remaining 334219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.980 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 153.430 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.230 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 40414 Z= 0.420 Angle : 0.852 16.481 54841 Z= 0.481 Chirality : 0.047 0.420 6243 Planarity : 0.005 0.091 6791 Dihedral : 15.493 170.731 15285 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.48 % Favored : 89.39 % Rotamer: Outliers : 0.38 % Allowed : 0.54 % Favored : 99.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4795 helix: -0.04 (0.10), residues: 2839 sheet: -1.56 (0.35), residues: 210 loop : -2.99 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A2196 HIS 0.012 0.001 HIS A2787 PHE 0.022 0.002 PHE A 531 TYR 0.023 0.002 TYR B 71 ARG 0.018 0.001 ARG A2530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 917 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6730 (mmt180) cc_final: 0.6520 (mpt-90) REVERT: A 80 GLU cc_start: 0.6275 (mp0) cc_final: 0.5794 (mp0) REVERT: A 165 LYS cc_start: 0.3880 (OUTLIER) cc_final: 0.3166 (tttt) REVERT: A 172 GLU cc_start: 0.7713 (tt0) cc_final: 0.7001 (tm-30) REVERT: A 210 SER cc_start: 0.7594 (t) cc_final: 0.7105 (m) REVERT: A 214 GLU cc_start: 0.6814 (tt0) cc_final: 0.6593 (tt0) REVERT: A 239 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6315 (mp0) REVERT: A 263 LYS cc_start: 0.7495 (mptt) cc_final: 0.6873 (mppt) REVERT: A 303 HIS cc_start: 0.5763 (t-90) cc_final: 0.5501 (t-90) REVERT: A 309 LYS cc_start: 0.6558 (ttmt) cc_final: 0.6221 (ttmm) REVERT: A 340 TYR cc_start: 0.6818 (t80) cc_final: 0.6342 (t80) REVERT: A 342 MET cc_start: 0.6828 (mmp) cc_final: 0.6479 (mmt) REVERT: A 351 ASN cc_start: 0.6831 (t0) cc_final: 0.6545 (t0) REVERT: A 373 CYS cc_start: 0.6544 (m) cc_final: 0.6106 (m) REVERT: A 438 LEU cc_start: 0.7766 (mp) cc_final: 0.7506 (mm) REVERT: A 466 LEU cc_start: 0.6011 (tt) cc_final: 0.5777 (mt) REVERT: A 534 LEU cc_start: 0.6399 (mt) cc_final: 0.6174 (mt) REVERT: A 578 LYS cc_start: 0.6680 (ptpt) cc_final: 0.6296 (ptpp) REVERT: A 633 ILE cc_start: 0.7376 (mm) cc_final: 0.7126 (mm) REVERT: A 672 ILE cc_start: 0.7737 (mt) cc_final: 0.7380 (mp) REVERT: A 701 TYR cc_start: 0.6183 (m-80) cc_final: 0.5930 (m-80) REVERT: A 720 GLN cc_start: 0.6151 (mm-40) cc_final: 0.5935 (mm110) REVERT: A 775 GLU cc_start: 0.7008 (tt0) cc_final: 0.6019 (mt-10) REVERT: A 781 ASP cc_start: 0.6787 (m-30) cc_final: 0.6307 (m-30) REVERT: A 823 GLN cc_start: 0.6053 (tt0) cc_final: 0.5630 (mm-40) REVERT: A 849 GLU cc_start: 0.5301 (pm20) cc_final: 0.5015 (pt0) REVERT: A 857 GLN cc_start: 0.6391 (mt0) cc_final: 0.5738 (mm110) REVERT: A 865 GLN cc_start: 0.6754 (mt0) cc_final: 0.6205 (mt0) REVERT: A 881 LYS cc_start: 0.5972 (mttp) cc_final: 0.5417 (mmmt) REVERT: A 889 GLU cc_start: 0.6280 (tm-30) cc_final: 0.5437 (tp30) REVERT: A 916 GLU cc_start: 0.6463 (mp0) cc_final: 0.6107 (tt0) REVERT: A 989 MET cc_start: 0.5867 (mmt) cc_final: 0.5651 (mmm) REVERT: A 1015 ASP cc_start: 0.5591 (m-30) cc_final: 0.5178 (m-30) REVERT: A 1084 ASN cc_start: 0.6108 (m-40) cc_final: 0.5887 (m110) REVERT: A 1087 ARG cc_start: 0.4839 (ttm170) cc_final: 0.4232 (mtp85) REVERT: A 1136 ARG cc_start: 0.5004 (ptp90) cc_final: 0.4080 (ptp90) REVERT: A 1185 HIS cc_start: 0.4774 (t-90) cc_final: 0.4517 (t-170) REVERT: A 1489 LYS cc_start: 0.5212 (ttmm) cc_final: 0.4943 (mttp) REVERT: A 1509 GLN cc_start: 0.5593 (tt0) cc_final: 0.4810 (tp-100) REVERT: A 1576 ASP cc_start: 0.6025 (p0) cc_final: 0.5645 (m-30) REVERT: A 1592 MET cc_start: 0.6600 (tpt) cc_final: 0.5937 (tpt) REVERT: A 1607 GLU cc_start: 0.5757 (mm-30) cc_final: 0.5412 (tp30) REVERT: A 1614 GLN cc_start: 0.5572 (tt0) cc_final: 0.5233 (tt0) REVERT: A 1740 VAL cc_start: 0.4954 (t) cc_final: 0.4753 (t) REVERT: A 1762 MET cc_start: 0.4582 (mmp) cc_final: 0.4159 (mmp) REVERT: A 1795 VAL cc_start: 0.6179 (t) cc_final: 0.5766 (t) REVERT: A 1799 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5366 (mt-10) REVERT: A 1804 MET cc_start: 0.5614 (mtp) cc_final: 0.5194 (mtp) REVERT: A 1849 ASP cc_start: 0.6440 (t0) cc_final: 0.5223 (m-30) REVERT: A 1869 LYS cc_start: 0.5807 (mmmm) cc_final: 0.5527 (mmtm) REVERT: A 1936 ARG cc_start: 0.5904 (mmm160) cc_final: 0.5634 (mmm160) REVERT: A 1949 ILE cc_start: 0.6261 (mt) cc_final: 0.5853 (mt) REVERT: A 1971 PRO cc_start: 0.3950 (Cg_endo) cc_final: 0.3635 (Cg_exo) REVERT: A 2085 MET cc_start: 0.6027 (pmm) cc_final: 0.5566 (pmm) REVERT: A 2162 LYS cc_start: 0.7362 (mttp) cc_final: 0.7075 (mmtm) REVERT: A 2163 HIS cc_start: 0.6394 (m-70) cc_final: 0.5691 (m-70) REVERT: A 2170 GLN cc_start: 0.6504 (tt0) cc_final: 0.6288 (tt0) REVERT: A 2220 MET cc_start: 0.6461 (mtm) cc_final: 0.6205 (mtt) REVERT: A 2221 LYS cc_start: 0.5166 (tttm) cc_final: 0.4852 (tppp) REVERT: A 2230 VAL cc_start: 0.6051 (m) cc_final: 0.5679 (p) REVERT: A 2232 ARG cc_start: 0.6508 (ttm170) cc_final: 0.6129 (mtp85) REVERT: A 2239 LYS cc_start: 0.6287 (tmmt) cc_final: 0.5941 (ttpt) REVERT: A 2243 GLU cc_start: 0.6285 (tm-30) cc_final: 0.6001 (pt0) REVERT: A 2309 PHE cc_start: 0.7918 (m-80) cc_final: 0.7601 (m-80) REVERT: A 2356 MET cc_start: 0.5481 (mtm) cc_final: 0.5267 (mtp) REVERT: A 2357 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5446 (mp0) REVERT: A 2369 LYS cc_start: 0.7436 (mttt) cc_final: 0.6329 (mmpt) REVERT: A 2379 MET cc_start: 0.7635 (tpp) cc_final: 0.7199 (tpt) REVERT: A 2414 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7163 (mm-40) REVERT: A 2430 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6451 (tt0) REVERT: A 2434 VAL cc_start: 0.6981 (t) cc_final: 0.6780 (p) REVERT: A 2437 ASP cc_start: 0.5945 (m-30) cc_final: 0.5551 (m-30) REVERT: A 2445 LYS cc_start: 0.7568 (mmtp) cc_final: 0.7244 (ttmt) REVERT: A 2447 LYS cc_start: 0.7954 (mmpt) cc_final: 0.7507 (mmpt) REVERT: A 2498 ILE cc_start: 0.7337 (pt) cc_final: 0.7126 (pp) REVERT: A 2519 LEU cc_start: 0.6631 (tp) cc_final: 0.6425 (tp) REVERT: A 2522 ARG cc_start: 0.5786 (tmt170) cc_final: 0.5176 (ttm-80) REVERT: A 2568 MET cc_start: 0.5317 (ptm) cc_final: 0.4951 (ptt) REVERT: A 2571 ASP cc_start: 0.6078 (m-30) cc_final: 0.5722 (m-30) REVERT: A 2806 LYS cc_start: 0.6877 (tmtt) cc_final: 0.6633 (tttm) REVERT: A 2818 LYS cc_start: 0.7593 (tttt) cc_final: 0.6573 (tmmt) REVERT: A 2824 LYS cc_start: 0.6444 (ttmt) cc_final: 0.5874 (tttt) REVERT: A 2856 SER cc_start: 0.8273 (p) cc_final: 0.7342 (t) REVERT: A 2864 GLN cc_start: 0.6857 (mm-40) cc_final: 0.5877 (tm-30) REVERT: A 2951 GLN cc_start: 0.6047 (tp40) cc_final: 0.5382 (pm20) REVERT: A 2990 GLU cc_start: 0.6957 (tt0) cc_final: 0.6447 (tt0) REVERT: A 2995 GLU cc_start: 0.7338 (tt0) cc_final: 0.6975 (tt0) REVERT: A 3067 LYS cc_start: 0.6843 (ptmm) cc_final: 0.6311 (pttp) REVERT: A 3090 TYR cc_start: 0.7675 (m-80) cc_final: 0.6545 (m-80) REVERT: A 3238 MET cc_start: 0.7470 (mtm) cc_final: 0.6813 (mtp) REVERT: A 3289 ARG cc_start: 0.6892 (mpt90) cc_final: 0.6201 (mpt-90) REVERT: A 3414 MET cc_start: 0.5556 (mmm) cc_final: 0.5309 (mmm) REVERT: A 3442 TYR cc_start: 0.5436 (m-10) cc_final: 0.5117 (m-80) REVERT: A 3460 GLU cc_start: 0.5819 (pm20) cc_final: 0.5224 (tm-30) REVERT: A 3582 GLU cc_start: 0.5563 (mp0) cc_final: 0.5291 (mt-10) REVERT: A 3712 LEU cc_start: 0.5991 (mp) cc_final: 0.5390 (tp) REVERT: A 3718 ARG cc_start: 0.4891 (mpp80) cc_final: 0.4570 (mpp80) REVERT: A 3729 MET cc_start: 0.4595 (mtp) cc_final: 0.4362 (ttm) REVERT: A 3750 PHE cc_start: 0.7292 (m-80) cc_final: 0.7088 (m-80) REVERT: A 3796 MET cc_start: 0.6659 (mmp) cc_final: 0.6249 (mmm) REVERT: A 3813 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6813 (tttt) REVERT: A 3814 ASP cc_start: 0.6008 (m-30) cc_final: 0.5539 (m-30) REVERT: A 3818 ASN cc_start: 0.5985 (p0) cc_final: 0.5651 (p0) REVERT: A 3858 MET cc_start: 0.6917 (tmm) cc_final: 0.6672 (tmm) REVERT: A 3932 MET cc_start: 0.7762 (mmm) cc_final: 0.7345 (tpt) REVERT: A 3941 ASP cc_start: 0.6882 (t0) cc_final: 0.6619 (t0) REVERT: A 3951 GLN cc_start: 0.5330 (tt0) cc_final: 0.4358 (tm-30) REVERT: A 4007 LYS cc_start: 0.5310 (mmmt) cc_final: 0.4551 (mtpt) REVERT: A 4062 ASP cc_start: 0.5494 (m-30) cc_final: 0.5038 (m-30) REVERT: A 4082 ARG cc_start: 0.4658 (ttm110) cc_final: 0.4391 (ttm-80) REVERT: B 61 ASP cc_start: 0.6872 (t0) cc_final: 0.6535 (t70) REVERT: B 78 SER cc_start: 0.7516 (m) cc_final: 0.7285 (m) REVERT: B 99 PHE cc_start: 0.7615 (m-80) cc_final: 0.7052 (m-80) REVERT: B 109 ASP cc_start: 0.6968 (t70) cc_final: 0.6667 (t0) REVERT: B 128 GLN cc_start: 0.5664 (tm-30) cc_final: 0.5456 (tm-30) REVERT: B 130 ARG cc_start: 0.5722 (mtp85) cc_final: 0.5479 (mtp180) REVERT: B 160 LYS cc_start: 0.6948 (tppp) cc_final: 0.6427 (tmtt) REVERT: B 165 ARG cc_start: 0.6480 (ttp-110) cc_final: 0.5987 (mtp85) REVERT: B 182 LYS cc_start: 0.4909 (OUTLIER) cc_final: 0.4103 (ttpp) REVERT: B 192 ASP cc_start: 0.5558 (t70) cc_final: 0.5245 (t70) REVERT: B 294 GLU cc_start: 0.6226 (mm-30) cc_final: 0.5709 (mt-10) REVERT: B 317 LYS cc_start: 0.4922 (mttt) cc_final: 0.4632 (mtmt) REVERT: B 336 GLU cc_start: 0.6329 (pp20) cc_final: 0.5920 (pt0) REVERT: B 346 MET cc_start: 0.5915 (mtm) cc_final: 0.5616 (mtm) REVERT: B 393 GLU cc_start: 0.5770 (mp0) cc_final: 0.5396 (tt0) REVERT: B 445 LYS cc_start: 0.5421 (mttm) cc_final: 0.5072 (mttp) REVERT: B 479 GLU cc_start: 0.7112 (pm20) cc_final: 0.6843 (pt0) REVERT: B 499 GLU cc_start: 0.6738 (pm20) cc_final: 0.6521 (pm20) REVERT: C 90 LEU cc_start: 0.3937 (mm) cc_final: 0.3698 (mp) REVERT: C 210 MET cc_start: 0.5628 (ppp) cc_final: 0.4893 (tpt) REVERT: C 233 LYS cc_start: 0.3907 (mttt) cc_final: 0.3126 (mmtt) REVERT: C 271 ARG cc_start: 0.6458 (mtt-85) cc_final: 0.6148 (ptp-110) REVERT: C 275 THR cc_start: 0.7275 (p) cc_final: 0.6997 (t) REVERT: C 287 GLU cc_start: 0.7055 (mp0) cc_final: 0.6805 (mm-30) REVERT: C 302 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6029 (mt-10) REVERT: C 304 GLU cc_start: 0.6381 (tt0) cc_final: 0.6137 (tt0) REVERT: C 309 ASP cc_start: 0.6492 (t0) cc_final: 0.6142 (t0) REVERT: C 315 ARG cc_start: 0.6540 (tpp-160) cc_final: 0.6229 (tpp80) REVERT: C 336 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6081 (pp20) REVERT: C 731 MET cc_start: 0.4021 (ptt) cc_final: 0.3728 (ptp) outliers start: 14 outliers final: 5 residues processed: 926 average time/residue: 1.4872 time to fit residues: 1698.2353 Evaluate side-chains 700 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 692 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 947 GLN Chi-restraints excluded: chain A residue 1880 MET Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 302 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 411 optimal weight: 0.7980 chunk 369 optimal weight: 0.4980 chunk 204 optimal weight: 0.8980 chunk 126 optimal weight: 0.0970 chunk 248 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 381 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 chunk 442 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 442 GLN A 484 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 GLN A 947 GLN A1069 HIS A1083 ASN ** A1146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 GLN A1980 ASN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3059 GLN A3093 GLN A3154 GLN A3296 GLN A3516 HIS A3524 ASN ** A3551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 359 HIS ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 40414 Z= 0.263 Angle : 0.733 11.466 54841 Z= 0.370 Chirality : 0.044 0.235 6243 Planarity : 0.005 0.069 6791 Dihedral : 12.554 168.897 5786 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.04 % Favored : 89.90 % Rotamer: Outliers : 2.43 % Allowed : 11.33 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 4795 helix: 0.28 (0.10), residues: 2843 sheet: -1.36 (0.36), residues: 203 loop : -2.82 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2196 HIS 0.007 0.001 HIS A1115 PHE 0.038 0.002 PHE A2260 TYR 0.022 0.002 TYR A 366 ARG 0.026 0.001 ARG A3282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 752 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6778 (mmt180) cc_final: 0.6371 (mpt90) REVERT: A 77 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7048 (mp0) REVERT: A 80 GLU cc_start: 0.6187 (mp0) cc_final: 0.5760 (mp0) REVERT: A 165 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.4910 (tttt) REVERT: A 172 GLU cc_start: 0.8154 (tt0) cc_final: 0.7187 (tm-30) REVERT: A 191 ASN cc_start: 0.7441 (m-40) cc_final: 0.7193 (m110) REVERT: A 214 GLU cc_start: 0.6938 (tt0) cc_final: 0.6731 (tt0) REVERT: A 239 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6471 (mp0) REVERT: A 263 LYS cc_start: 0.7685 (mptt) cc_final: 0.6962 (mppt) REVERT: A 307 GLU cc_start: 0.7103 (tt0) cc_final: 0.6836 (tt0) REVERT: A 309 LYS cc_start: 0.6475 (ttmt) cc_final: 0.6182 (tttt) REVERT: A 329 LYS cc_start: 0.6598 (mtmp) cc_final: 0.6315 (mtmm) REVERT: A 340 TYR cc_start: 0.6936 (t80) cc_final: 0.6696 (t80) REVERT: A 342 MET cc_start: 0.6982 (mmp) cc_final: 0.6632 (mmt) REVERT: A 373 CYS cc_start: 0.7069 (m) cc_final: 0.6621 (m) REVERT: A 448 GLN cc_start: 0.6981 (mm110) cc_final: 0.6602 (mm110) REVERT: A 453 MET cc_start: 0.6553 (tpp) cc_final: 0.6348 (tpp) REVERT: A 476 ARG cc_start: 0.5877 (mtp-110) cc_final: 0.5521 (mtp-110) REVERT: A 578 LYS cc_start: 0.6940 (ptpt) cc_final: 0.6504 (ptpp) REVERT: A 631 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.4337 (ttm110) REVERT: A 632 GLU cc_start: 0.5327 (mt-10) cc_final: 0.5101 (mt-10) REVERT: A 652 GLU cc_start: 0.5310 (tp30) cc_final: 0.5098 (mm-30) REVERT: A 720 GLN cc_start: 0.6776 (mm-40) cc_final: 0.6525 (mm-40) REVERT: A 746 ARG cc_start: 0.7124 (ttp-170) cc_final: 0.6877 (mtm180) REVERT: A 775 GLU cc_start: 0.6971 (tt0) cc_final: 0.6161 (mt-10) REVERT: A 781 ASP cc_start: 0.6727 (m-30) cc_final: 0.6260 (m-30) REVERT: A 784 VAL cc_start: 0.6486 (m) cc_final: 0.6218 (p) REVERT: A 785 MET cc_start: 0.6792 (mmm) cc_final: 0.6418 (mmm) REVERT: A 823 GLN cc_start: 0.6066 (tt0) cc_final: 0.5676 (mm-40) REVERT: A 828 LYS cc_start: 0.6738 (mmmm) cc_final: 0.6066 (mttp) REVERT: A 849 GLU cc_start: 0.5448 (pm20) cc_final: 0.5153 (pt0) REVERT: A 851 ILE cc_start: 0.7135 (mm) cc_final: 0.6841 (mm) REVERT: A 857 GLN cc_start: 0.6562 (mt0) cc_final: 0.5713 (mm110) REVERT: A 858 MET cc_start: 0.6114 (tpp) cc_final: 0.5167 (tpp) REVERT: A 865 GLN cc_start: 0.6851 (mt0) cc_final: 0.6268 (mt0) REVERT: A 881 LYS cc_start: 0.6102 (mttp) cc_final: 0.5408 (mmmt) REVERT: A 889 GLU cc_start: 0.6361 (tm-30) cc_final: 0.5589 (tp30) REVERT: A 983 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6031 (mm) REVERT: A 989 MET cc_start: 0.5917 (mmt) cc_final: 0.5681 (mmm) REVERT: A 1031 ARG cc_start: 0.6374 (mtp85) cc_final: 0.5764 (ttp-170) REVERT: A 1136 ARG cc_start: 0.5476 (ptp90) cc_final: 0.4498 (mtt90) REVERT: A 1185 HIS cc_start: 0.4888 (t-90) cc_final: 0.4566 (t70) REVERT: A 1332 TYR cc_start: 0.4567 (t80) cc_final: 0.4030 (t80) REVERT: A 1403 MET cc_start: 0.5907 (mtt) cc_final: 0.5688 (mmt) REVERT: A 1509 GLN cc_start: 0.5631 (tt0) cc_final: 0.4749 (tp-100) REVERT: A 1576 ASP cc_start: 0.5458 (p0) cc_final: 0.5127 (m-30) REVERT: A 1586 SER cc_start: 0.7941 (m) cc_final: 0.7687 (m) REVERT: A 1592 MET cc_start: 0.6957 (tpt) cc_final: 0.6292 (tpt) REVERT: A 1607 GLU cc_start: 0.6002 (mm-30) cc_final: 0.5539 (mm-30) REVERT: A 1614 GLN cc_start: 0.5558 (tt0) cc_final: 0.5346 (tt0) REVERT: A 1735 ARG cc_start: 0.5666 (mtp85) cc_final: 0.5080 (ptm160) REVERT: A 1762 MET cc_start: 0.4533 (mmp) cc_final: 0.4206 (mmp) REVERT: A 1775 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4703 (mt-10) REVERT: A 1795 VAL cc_start: 0.6168 (t) cc_final: 0.5846 (t) REVERT: A 1799 GLU cc_start: 0.5696 (mt-10) cc_final: 0.5383 (mt-10) REVERT: A 1829 TRP cc_start: 0.5537 (m100) cc_final: 0.5151 (m100) REVERT: A 1849 ASP cc_start: 0.6036 (t0) cc_final: 0.4980 (m-30) REVERT: A 1917 LYS cc_start: 0.5367 (tppt) cc_final: 0.5062 (tppt) REVERT: A 1921 ASP cc_start: 0.5214 (OUTLIER) cc_final: 0.4549 (p0) REVERT: A 1971 PRO cc_start: 0.3952 (Cg_endo) cc_final: 0.3681 (Cg_exo) REVERT: A 2085 MET cc_start: 0.6027 (pmm) cc_final: 0.5539 (pmm) REVERT: A 2104 MET cc_start: 0.5694 (ptt) cc_final: 0.5494 (ptp) REVERT: A 2127 LYS cc_start: 0.5915 (mptt) cc_final: 0.5686 (mptt) REVERT: A 2162 LYS cc_start: 0.7457 (mttp) cc_final: 0.7136 (mmtm) REVERT: A 2163 HIS cc_start: 0.6459 (m-70) cc_final: 0.5648 (m-70) REVERT: A 2170 GLN cc_start: 0.6556 (tt0) cc_final: 0.6314 (tt0) REVERT: A 2220 MET cc_start: 0.6474 (mtm) cc_final: 0.6130 (mtt) REVERT: A 2221 LYS cc_start: 0.5463 (tttm) cc_final: 0.5193 (tppp) REVERT: A 2239 LYS cc_start: 0.6247 (tmmt) cc_final: 0.5843 (ttpt) REVERT: A 2243 GLU cc_start: 0.6320 (tm-30) cc_final: 0.6004 (pt0) REVERT: A 2292 CYS cc_start: 0.6368 (t) cc_final: 0.5537 (p) REVERT: A 2329 TYR cc_start: 0.7559 (t80) cc_final: 0.7257 (t80) REVERT: A 2356 MET cc_start: 0.5801 (mtm) cc_final: 0.5549 (mtp) REVERT: A 2357 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5822 (mp0) REVERT: A 2369 LYS cc_start: 0.7674 (mttt) cc_final: 0.6556 (mmpt) REVERT: A 2414 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7002 (mm-40) REVERT: A 2427 ARG cc_start: 0.6607 (tpt90) cc_final: 0.5925 (tpm-80) REVERT: A 2428 ASP cc_start: 0.6170 (t70) cc_final: 0.5630 (t70) REVERT: A 2430 GLU cc_start: 0.6134 (mm-30) cc_final: 0.5661 (tt0) REVERT: A 2434 VAL cc_start: 0.7234 (t) cc_final: 0.7013 (p) REVERT: A 2445 LYS cc_start: 0.7661 (mmtp) cc_final: 0.7311 (ttmt) REVERT: A 2447 LYS cc_start: 0.7835 (mmpt) cc_final: 0.7515 (mmtt) REVERT: A 2498 ILE cc_start: 0.7166 (pt) cc_final: 0.6899 (pp) REVERT: A 2522 ARG cc_start: 0.5688 (tmt170) cc_final: 0.5256 (ttm-80) REVERT: A 2565 MET cc_start: 0.6111 (mmp) cc_final: 0.5874 (mmp) REVERT: A 2795 GLN cc_start: 0.6345 (tm-30) cc_final: 0.5938 (tp40) REVERT: A 2818 LYS cc_start: 0.7738 (tttt) cc_final: 0.6672 (tmmt) REVERT: A 2839 ASP cc_start: 0.5891 (m-30) cc_final: 0.5521 (m-30) REVERT: A 2864 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6014 (tm-30) REVERT: A 2990 GLU cc_start: 0.6905 (tt0) cc_final: 0.6545 (tt0) REVERT: A 2995 GLU cc_start: 0.7292 (tt0) cc_final: 0.6890 (tt0) REVERT: A 3059 GLN cc_start: 0.6961 (mm110) cc_final: 0.6749 (mm-40) REVERT: A 3067 LYS cc_start: 0.6800 (ptmm) cc_final: 0.6208 (pttp) REVERT: A 3090 TYR cc_start: 0.7678 (m-80) cc_final: 0.6368 (m-80) REVERT: A 3140 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6288 (mt-10) REVERT: A 3172 LYS cc_start: 0.7881 (ttmm) cc_final: 0.6351 (tptp) REVERT: A 3173 MET cc_start: 0.7497 (mmm) cc_final: 0.7189 (mpp) REVERT: A 3176 MET cc_start: 0.8378 (mmm) cc_final: 0.7888 (mmm) REVERT: A 3237 SER cc_start: 0.7084 (t) cc_final: 0.6796 (m) REVERT: A 3238 MET cc_start: 0.7667 (mtm) cc_final: 0.7030 (mtp) REVERT: A 3270 ASP cc_start: 0.5867 (t70) cc_final: 0.5658 (t70) REVERT: A 3284 SER cc_start: 0.7789 (p) cc_final: 0.7554 (p) REVERT: A 3287 ARG cc_start: 0.6532 (ptm160) cc_final: 0.6054 (ptm-80) REVERT: A 3289 ARG cc_start: 0.6730 (mpt90) cc_final: 0.6068 (mpt-90) REVERT: A 3293 CYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4998 (p) REVERT: A 3442 TYR cc_start: 0.5740 (m-10) cc_final: 0.5423 (m-10) REVERT: A 3516 HIS cc_start: 0.5866 (t-170) cc_final: 0.5653 (t-90) REVERT: A 3704 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6146 (mp10) REVERT: A 3718 ARG cc_start: 0.5255 (mpp80) cc_final: 0.4949 (mpp80) REVERT: A 3747 GLU cc_start: 0.6954 (tt0) cc_final: 0.6720 (tt0) REVERT: A 3750 PHE cc_start: 0.7442 (m-80) cc_final: 0.7081 (m-80) REVERT: A 3766 GLN cc_start: 0.6440 (pt0) cc_final: 0.5810 (pp30) REVERT: A 3772 ASN cc_start: 0.6131 (p0) cc_final: 0.5849 (p0) REVERT: A 3796 MET cc_start: 0.7442 (mmp) cc_final: 0.6887 (mmm) REVERT: A 3932 MET cc_start: 0.7672 (mmm) cc_final: 0.7401 (mmm) REVERT: A 3951 GLN cc_start: 0.5966 (tt0) cc_final: 0.5720 (tt0) REVERT: A 3974 MET cc_start: 0.7365 (mpp) cc_final: 0.7075 (mpt) REVERT: A 4007 LYS cc_start: 0.5512 (mmmt) cc_final: 0.4577 (mtpt) REVERT: A 4062 ASP cc_start: 0.5815 (m-30) cc_final: 0.5297 (m-30) REVERT: A 4082 ARG cc_start: 0.4650 (ttm110) cc_final: 0.4353 (ttm-80) REVERT: A 4108 MET cc_start: 0.7593 (ttm) cc_final: 0.7307 (mtt) REVERT: B 61 ASP cc_start: 0.7299 (t0) cc_final: 0.6840 (t70) REVERT: B 78 SER cc_start: 0.7665 (m) cc_final: 0.7375 (m) REVERT: B 101 ASN cc_start: 0.6391 (m-40) cc_final: 0.6070 (m-40) REVERT: B 109 ASP cc_start: 0.6952 (t70) cc_final: 0.6671 (t0) REVERT: B 160 LYS cc_start: 0.7245 (tppp) cc_final: 0.6712 (tmtt) REVERT: B 165 ARG cc_start: 0.6829 (ttp-110) cc_final: 0.6160 (mtp85) REVERT: B 192 ASP cc_start: 0.5548 (t70) cc_final: 0.5343 (t70) REVERT: B 294 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5872 (mt-10) REVERT: B 335 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6382 (tt0) REVERT: B 342 ASP cc_start: 0.7810 (m-30) cc_final: 0.6673 (t70) REVERT: B 453 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7065 (mmp) REVERT: B 479 GLU cc_start: 0.7267 (pm20) cc_final: 0.6903 (pt0) REVERT: B 499 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6397 (pm20) REVERT: C 20 MET cc_start: 0.3099 (tmt) cc_final: 0.2856 (tmt) REVERT: C 92 GLU cc_start: 0.6006 (pp20) cc_final: 0.5513 (pm20) REVERT: C 210 MET cc_start: 0.5730 (ppp) cc_final: 0.5002 (tpt) REVERT: C 233 LYS cc_start: 0.4049 (mttt) cc_final: 0.3223 (mmtt) REVERT: C 246 HIS cc_start: 0.6045 (p90) cc_final: 0.5095 (p-80) REVERT: C 259 ILE cc_start: 0.6102 (OUTLIER) cc_final: 0.5749 (tt) REVERT: C 271 ARG cc_start: 0.6396 (mtt-85) cc_final: 0.6038 (ptp-110) REVERT: C 273 LYS cc_start: 0.6795 (ttmm) cc_final: 0.6530 (ttmm) REVERT: C 275 THR cc_start: 0.7382 (p) cc_final: 0.7021 (t) REVERT: C 286 LYS cc_start: 0.6434 (ttpt) cc_final: 0.5995 (ttpp) REVERT: C 287 GLU cc_start: 0.7080 (mp0) cc_final: 0.6531 (mp0) REVERT: C 288 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.6004 (m-30) REVERT: C 301 ASP cc_start: 0.5772 (p0) cc_final: 0.5511 (p0) REVERT: C 302 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5695 (mt-10) REVERT: C 304 GLU cc_start: 0.7157 (tt0) cc_final: 0.6879 (tt0) REVERT: C 309 ASP cc_start: 0.6729 (t0) cc_final: 0.6410 (t0) REVERT: C 315 ARG cc_start: 0.6744 (tpp-160) cc_final: 0.6355 (tpp80) REVERT: C 336 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6184 (pp20) REVERT: C 371 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5504 (pp20) REVERT: C 409 PHE cc_start: 0.4885 (m-80) cc_final: 0.4573 (m-80) REVERT: C 474 GLU cc_start: 0.6493 (tm-30) cc_final: 0.6199 (tm-30) REVERT: C 731 MET cc_start: 0.3478 (ptt) cc_final: 0.3166 (ptp) outliers start: 101 outliers final: 31 residues processed: 797 average time/residue: 1.5109 time to fit residues: 1493.6802 Evaluate side-chains 721 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 677 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1452 VAL Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1921 ASP Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2340 SER Chi-restraints excluded: chain A residue 2780 LEU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 3227 ILE Chi-restraints excluded: chain A residue 3293 CYS Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3704 GLN Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 245 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 368 optimal weight: 0.5980 chunk 301 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 443 optimal weight: 3.9990 chunk 478 optimal weight: 20.0000 chunk 394 optimal weight: 2.9990 chunk 439 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 415 GLN A 533 HIS A 925 GLN ** A1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1613 HIS ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2213 ASN A2266 ASN A3093 GLN A3263 HIS A3339 ASN A3524 ASN ** A3551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 HIS A3951 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS C 415 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 40414 Z= 0.405 Angle : 0.824 12.390 54841 Z= 0.414 Chirality : 0.049 0.284 6243 Planarity : 0.006 0.072 6791 Dihedral : 12.524 172.856 5774 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.54 % Favored : 89.42 % Rotamer: Outliers : 3.71 % Allowed : 14.04 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4795 helix: 0.07 (0.10), residues: 2853 sheet: -1.20 (0.35), residues: 200 loop : -2.80 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A2196 HIS 0.007 0.001 HIS A3986 PHE 0.047 0.003 PHE A2260 TYR 0.040 0.003 TYR B 71 ARG 0.012 0.001 ARG A 913 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 736 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7032 (mm) REVERT: A 77 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7127 (mp0) REVERT: A 80 GLU cc_start: 0.6278 (mp0) cc_final: 0.5895 (mp0) REVERT: A 146 GLU cc_start: 0.6062 (tp30) cc_final: 0.5708 (tm-30) REVERT: A 165 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.4624 (tttm) REVERT: A 191 ASN cc_start: 0.7679 (m-40) cc_final: 0.7305 (m110) REVERT: A 207 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7972 (tp40) REVERT: A 239 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6343 (mp0) REVERT: A 243 GLN cc_start: 0.6098 (tp40) cc_final: 0.5405 (mp10) REVERT: A 263 LYS cc_start: 0.7260 (mptt) cc_final: 0.6617 (mppt) REVERT: A 307 GLU cc_start: 0.6918 (tt0) cc_final: 0.6618 (tt0) REVERT: A 329 LYS cc_start: 0.6866 (mtmp) cc_final: 0.6487 (mtmm) REVERT: A 340 TYR cc_start: 0.6678 (t80) cc_final: 0.6192 (t80) REVERT: A 342 MET cc_start: 0.6973 (mmp) cc_final: 0.6670 (mmt) REVERT: A 343 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5900 (mm-30) REVERT: A 345 PHE cc_start: 0.6775 (m-10) cc_final: 0.6568 (m-10) REVERT: A 373 CYS cc_start: 0.7246 (m) cc_final: 0.6544 (m) REVERT: A 379 LYS cc_start: 0.6332 (mttm) cc_final: 0.5998 (mtpm) REVERT: A 395 MET cc_start: 0.6343 (ptm) cc_final: 0.5815 (ptm) REVERT: A 423 TYR cc_start: 0.7278 (m-80) cc_final: 0.6291 (m-80) REVERT: A 476 ARG cc_start: 0.6034 (mtp-110) cc_final: 0.5744 (ttm110) REVERT: A 480 SER cc_start: 0.7167 (m) cc_final: 0.6928 (p) REVERT: A 578 LYS cc_start: 0.7061 (ptpt) cc_final: 0.6543 (ptpp) REVERT: A 662 LEU cc_start: 0.7405 (mp) cc_final: 0.7189 (mm) REVERT: A 669 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6820 (mp) REVERT: A 720 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7176 (mm-40) REVERT: A 746 ARG cc_start: 0.7359 (ttp-170) cc_final: 0.7100 (mtm180) REVERT: A 775 GLU cc_start: 0.6811 (tt0) cc_final: 0.5928 (mp0) REVERT: A 781 ASP cc_start: 0.6761 (m-30) cc_final: 0.6247 (m-30) REVERT: A 784 VAL cc_start: 0.6261 (m) cc_final: 0.5923 (p) REVERT: A 823 GLN cc_start: 0.5997 (tt0) cc_final: 0.5320 (mm-40) REVERT: A 828 LYS cc_start: 0.6901 (mmmm) cc_final: 0.6315 (mttp) REVERT: A 849 GLU cc_start: 0.5581 (pm20) cc_final: 0.5227 (pt0) REVERT: A 857 GLN cc_start: 0.7097 (mt0) cc_final: 0.6176 (mm110) REVERT: A 879 MET cc_start: 0.7376 (ttm) cc_final: 0.7062 (ttm) REVERT: A 881 LYS cc_start: 0.6410 (mttp) cc_final: 0.5766 (mmmt) REVERT: A 889 GLU cc_start: 0.6428 (tm-30) cc_final: 0.5718 (tp30) REVERT: A 983 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6129 (mt) REVERT: A 989 MET cc_start: 0.5773 (mmt) cc_final: 0.5515 (mmm) REVERT: A 990 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: A 1015 ASP cc_start: 0.5818 (m-30) cc_final: 0.5317 (m-30) REVERT: A 1061 LYS cc_start: 0.6865 (mtpm) cc_final: 0.6518 (mtpp) REVERT: A 1076 LEU cc_start: 0.6222 (tp) cc_final: 0.5783 (tm) REVERT: A 1083 ASN cc_start: 0.5916 (t0) cc_final: 0.5711 (t0) REVERT: A 1125 GLN cc_start: 0.6743 (tp40) cc_final: 0.6400 (tp-100) REVERT: A 1136 ARG cc_start: 0.5379 (ptp90) cc_final: 0.4738 (mtt90) REVERT: A 1332 TYR cc_start: 0.4860 (t80) cc_final: 0.4416 (t80) REVERT: A 1509 GLN cc_start: 0.5794 (tt0) cc_final: 0.5142 (tp-100) REVERT: A 1576 ASP cc_start: 0.5153 (p0) cc_final: 0.4885 (m-30) REVERT: A 1602 ASP cc_start: 0.6130 (p0) cc_final: 0.5868 (p0) REVERT: A 1607 GLU cc_start: 0.6297 (mm-30) cc_final: 0.6018 (mm-30) REVERT: A 1608 ARG cc_start: 0.7115 (ptt-90) cc_final: 0.6901 (ptt90) REVERT: A 1627 LYS cc_start: 0.7055 (mmpt) cc_final: 0.6620 (mtmm) REVERT: A 1735 ARG cc_start: 0.5530 (mtp85) cc_final: 0.5318 (ptp-170) REVERT: A 1762 MET cc_start: 0.4785 (mmp) cc_final: 0.4438 (mmp) REVERT: A 1775 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.5068 (mt-10) REVERT: A 1799 GLU cc_start: 0.5778 (mt-10) cc_final: 0.5255 (mt-10) REVERT: A 1814 PHE cc_start: 0.4954 (t80) cc_final: 0.4695 (t80) REVERT: A 1849 ASP cc_start: 0.6325 (t0) cc_final: 0.5147 (m-30) REVERT: A 1917 LYS cc_start: 0.5373 (tppt) cc_final: 0.5118 (tppt) REVERT: A 1921 ASP cc_start: 0.4590 (OUTLIER) cc_final: 0.4068 (p0) REVERT: A 1971 PRO cc_start: 0.4020 (Cg_endo) cc_final: 0.3800 (Cg_exo) REVERT: A 2085 MET cc_start: 0.5968 (pmm) cc_final: 0.5616 (pmm) REVERT: A 2127 LYS cc_start: 0.5996 (mptt) cc_final: 0.5754 (mptt) REVERT: A 2162 LYS cc_start: 0.7483 (mttp) cc_final: 0.7177 (mmtm) REVERT: A 2170 GLN cc_start: 0.6308 (tt0) cc_final: 0.6075 (tt0) REVERT: A 2220 MET cc_start: 0.6464 (mtm) cc_final: 0.6169 (mtt) REVERT: A 2221 LYS cc_start: 0.5938 (tttm) cc_final: 0.5579 (ttmm) REVERT: A 2227 LYS cc_start: 0.6024 (tptt) cc_final: 0.5731 (tppp) REVERT: A 2239 LYS cc_start: 0.6409 (tmmt) cc_final: 0.5973 (ttpt) REVERT: A 2243 GLU cc_start: 0.6291 (tm-30) cc_final: 0.5732 (tm-30) REVERT: A 2292 CYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5659 (p) REVERT: A 2329 TYR cc_start: 0.7596 (t80) cc_final: 0.7394 (t80) REVERT: A 2341 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6823 (mt) REVERT: A 2356 MET cc_start: 0.6349 (mtm) cc_final: 0.6003 (mtp) REVERT: A 2357 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6398 (mp0) REVERT: A 2369 LYS cc_start: 0.7770 (mttt) cc_final: 0.6678 (mmpt) REVERT: A 2379 MET cc_start: 0.7506 (tpp) cc_final: 0.7252 (tpt) REVERT: A 2414 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6772 (mm-40) REVERT: A 2427 ARG cc_start: 0.6906 (tpt90) cc_final: 0.6360 (tpm-80) REVERT: A 2428 ASP cc_start: 0.6293 (t70) cc_final: 0.5833 (t70) REVERT: A 2430 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5682 (tt0) REVERT: A 2447 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7508 (mmpt) REVERT: A 2497 GLU cc_start: 0.6608 (tt0) cc_final: 0.6164 (tt0) REVERT: A 2498 ILE cc_start: 0.7290 (pt) cc_final: 0.6975 (pp) REVERT: A 2504 ASP cc_start: 0.6141 (m-30) cc_final: 0.5394 (m-30) REVERT: A 2522 ARG cc_start: 0.6018 (tmt170) cc_final: 0.5605 (ttm-80) REVERT: A 2536 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6740 (tt) REVERT: A 2795 GLN cc_start: 0.6625 (tm-30) cc_final: 0.6294 (tp40) REVERT: A 2818 LYS cc_start: 0.7676 (tttt) cc_final: 0.6975 (tttm) REVERT: A 2839 ASP cc_start: 0.6038 (m-30) cc_final: 0.5720 (m-30) REVERT: A 2978 LYS cc_start: 0.5653 (tttt) cc_final: 0.5432 (tttt) REVERT: A 2990 GLU cc_start: 0.7106 (tt0) cc_final: 0.6886 (tt0) REVERT: A 2995 GLU cc_start: 0.6892 (tt0) cc_final: 0.6682 (tt0) REVERT: A 3090 TYR cc_start: 0.7495 (m-80) cc_final: 0.6571 (m-80) REVERT: A 3140 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6801 (mt-10) REVERT: A 3147 LYS cc_start: 0.5955 (ttmt) cc_final: 0.5033 (tttp) REVERT: A 3158 LYS cc_start: 0.6650 (mtpp) cc_final: 0.6314 (mtpt) REVERT: A 3173 MET cc_start: 0.7498 (mmm) cc_final: 0.7020 (mpp) REVERT: A 3191 SER cc_start: 0.7646 (t) cc_final: 0.7426 (m) REVERT: A 3237 SER cc_start: 0.7168 (t) cc_final: 0.6824 (m) REVERT: A 3238 MET cc_start: 0.7835 (mtm) cc_final: 0.7226 (mtp) REVERT: A 3284 SER cc_start: 0.7627 (p) cc_final: 0.7335 (p) REVERT: A 3287 ARG cc_start: 0.6704 (ptm160) cc_final: 0.6118 (ptt90) REVERT: A 3289 ARG cc_start: 0.6528 (mpt90) cc_final: 0.5819 (mpt-90) REVERT: A 3293 CYS cc_start: 0.5570 (OUTLIER) cc_final: 0.5151 (p) REVERT: A 3327 ASN cc_start: 0.5747 (m-40) cc_final: 0.5183 (m110) REVERT: A 3335 ARG cc_start: 0.6231 (OUTLIER) cc_final: 0.5573 (ttt180) REVERT: A 3339 ASN cc_start: 0.5381 (m-40) cc_final: 0.5160 (m110) REVERT: A 3387 GLU cc_start: 0.6119 (tp30) cc_final: 0.5628 (tt0) REVERT: A 3582 GLU cc_start: 0.5918 (mp0) cc_final: 0.5549 (mt-10) REVERT: A 3704 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6632 (mt0) REVERT: A 3718 ARG cc_start: 0.5527 (mpp80) cc_final: 0.5118 (mpp80) REVERT: A 3734 ARG cc_start: 0.6131 (tpp80) cc_final: 0.5776 (ttm170) REVERT: A 3747 GLU cc_start: 0.7077 (tt0) cc_final: 0.6795 (tt0) REVERT: A 3766 GLN cc_start: 0.6765 (pt0) cc_final: 0.5926 (pp30) REVERT: A 3772 ASN cc_start: 0.7035 (p0) cc_final: 0.6719 (p0) REVERT: A 3799 ARG cc_start: 0.5468 (ptp-170) cc_final: 0.4846 (ptp-170) REVERT: A 3869 THR cc_start: 0.6603 (m) cc_final: 0.6210 (m) REVERT: A 3932 MET cc_start: 0.7702 (mmm) cc_final: 0.7365 (mmm) REVERT: A 3941 ASP cc_start: 0.7054 (t0) cc_final: 0.6421 (t70) REVERT: A 4082 ARG cc_start: 0.5043 (ttm110) cc_final: 0.4801 (ttm-80) REVERT: A 4108 MET cc_start: 0.7725 (ttm) cc_final: 0.7437 (mtt) REVERT: B 100 LYS cc_start: 0.6898 (mmpt) cc_final: 0.6693 (mptm) REVERT: B 109 ASP cc_start: 0.6812 (t70) cc_final: 0.6599 (t0) REVERT: B 145 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6144 (mt-10) REVERT: B 160 LYS cc_start: 0.7429 (tppp) cc_final: 0.6798 (tmtt) REVERT: B 161 MET cc_start: 0.8612 (mtm) cc_final: 0.8397 (mtt) REVERT: B 165 ARG cc_start: 0.6821 (ttp-110) cc_final: 0.5993 (mtp85) REVERT: B 187 ARG cc_start: 0.6966 (mtm-85) cc_final: 0.6580 (mtm-85) REVERT: B 192 ASP cc_start: 0.5755 (t70) cc_final: 0.5369 (t70) REVERT: B 258 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6313 (mtp85) REVERT: B 294 GLU cc_start: 0.6597 (mm-30) cc_final: 0.5968 (mt-10) REVERT: B 333 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6656 (mt-10) REVERT: B 335 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6817 (tt0) REVERT: B 341 ASP cc_start: 0.8316 (m-30) cc_final: 0.7980 (m-30) REVERT: B 361 TYR cc_start: 0.7194 (t80) cc_final: 0.6920 (t80) REVERT: B 393 GLU cc_start: 0.5877 (mp0) cc_final: 0.5288 (tt0) REVERT: B 443 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5653 (mtmt) REVERT: C 49 GLU cc_start: 0.5652 (OUTLIER) cc_final: 0.5314 (tm-30) REVERT: C 129 LYS cc_start: 0.7260 (mttt) cc_final: 0.7022 (mtpt) REVERT: C 210 MET cc_start: 0.5890 (ppp) cc_final: 0.5101 (tpt) REVERT: C 233 LYS cc_start: 0.4072 (mttt) cc_final: 0.3196 (mmtt) REVERT: C 271 ARG cc_start: 0.6563 (mtt-85) cc_final: 0.6151 (ptp-110) REVERT: C 273 LYS cc_start: 0.6912 (ttmm) cc_final: 0.6618 (ttmm) REVERT: C 275 THR cc_start: 0.7823 (p) cc_final: 0.7391 (t) REVERT: C 286 LYS cc_start: 0.6656 (ttpt) cc_final: 0.6216 (ttpp) REVERT: C 287 GLU cc_start: 0.7304 (mp0) cc_final: 0.6863 (mp0) REVERT: C 288 ASP cc_start: 0.6133 (OUTLIER) cc_final: 0.5904 (m-30) REVERT: C 302 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5618 (mt-10) REVERT: C 304 GLU cc_start: 0.7225 (tt0) cc_final: 0.6820 (tt0) REVERT: C 315 ARG cc_start: 0.6954 (tpp-160) cc_final: 0.6377 (tpp80) REVERT: C 332 LYS cc_start: 0.7239 (ptmt) cc_final: 0.6831 (ptmm) REVERT: C 336 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6336 (pp20) REVERT: C 343 LEU cc_start: 0.8138 (mt) cc_final: 0.7778 (mp) REVERT: C 371 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6237 (pp20) REVERT: C 430 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8011 (pp) REVERT: C 474 GLU cc_start: 0.6427 (tm-30) cc_final: 0.6106 (tm-30) REVERT: C 731 MET cc_start: 0.3714 (ptt) cc_final: 0.3261 (ptp) outliers start: 154 outliers final: 64 residues processed: 814 average time/residue: 1.4937 time to fit residues: 1495.1141 Evaluate side-chains 762 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 677 time to evaluate : 4.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1452 VAL Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1921 ASP Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2041 SER Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2292 CYS Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2536 LEU Chi-restraints excluded: chain A residue 2780 LEU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain A residue 3227 ILE Chi-restraints excluded: chain A residue 3262 LEU Chi-restraints excluded: chain A residue 3293 CYS Chi-restraints excluded: chain A residue 3330 LEU Chi-restraints excluded: chain A residue 3335 ARG Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3704 GLN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 437 optimal weight: 3.9990 chunk 333 optimal weight: 0.0050 chunk 229 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 211 optimal weight: 0.2980 chunk 297 optimal weight: 1.9990 chunk 444 optimal weight: 2.9990 chunk 470 optimal weight: 1.9990 chunk 232 optimal weight: 0.0970 chunk 421 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 overall best weight: 0.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 533 HIS A 613 HIS A 865 GLN A1004 GLN A1043 GLN A1589 ASN A1946 ASN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2275 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN A3383 GLN A3516 HIS A3524 ASN A3551 ASN A3766 GLN A3808 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 489 ASN C 298 ASN C 411 HIS C 432 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40414 Z= 0.191 Angle : 0.668 13.581 54841 Z= 0.336 Chirality : 0.042 0.195 6243 Planarity : 0.005 0.067 6791 Dihedral : 12.294 173.936 5773 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.29 % Favored : 90.69 % Rotamer: Outliers : 2.71 % Allowed : 17.37 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 4795 helix: 0.47 (0.10), residues: 2840 sheet: -1.02 (0.35), residues: 200 loop : -2.75 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2196 HIS 0.006 0.001 HIS A1367 PHE 0.025 0.001 PHE A1089 TYR 0.028 0.001 TYR A3442 ARG 0.011 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 714 time to evaluate : 4.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6893 (mmt180) cc_final: 0.6378 (mpt90) REVERT: A 77 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7142 (mp0) REVERT: A 80 GLU cc_start: 0.6252 (mp0) cc_final: 0.5911 (mp0) REVERT: A 165 LYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4235 (tttt) REVERT: A 172 GLU cc_start: 0.7860 (tt0) cc_final: 0.6794 (tm-30) REVERT: A 191 ASN cc_start: 0.7783 (m-40) cc_final: 0.7434 (m110) REVERT: A 239 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6721 (mp0) REVERT: A 243 GLN cc_start: 0.6068 (tp40) cc_final: 0.5378 (mp10) REVERT: A 263 LYS cc_start: 0.7176 (mptt) cc_final: 0.6554 (mppt) REVERT: A 307 GLU cc_start: 0.6867 (tt0) cc_final: 0.6634 (tt0) REVERT: A 329 LYS cc_start: 0.6880 (mtmp) cc_final: 0.6576 (mtmm) REVERT: A 340 TYR cc_start: 0.6602 (t80) cc_final: 0.6174 (t80) REVERT: A 373 CYS cc_start: 0.7086 (m) cc_final: 0.6469 (m) REVERT: A 379 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5790 (mtpm) REVERT: A 395 MET cc_start: 0.5950 (ptm) cc_final: 0.5476 (ptm) REVERT: A 415 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.6078 (mm-40) REVERT: A 423 TYR cc_start: 0.7209 (m-80) cc_final: 0.6306 (m-80) REVERT: A 441 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5769 (ttt) REVERT: A 524 TYR cc_start: 0.6958 (p90) cc_final: 0.6699 (p90) REVERT: A 578 LYS cc_start: 0.7066 (ptpt) cc_final: 0.6574 (ptpp) REVERT: A 662 LEU cc_start: 0.7457 (mp) cc_final: 0.7240 (mm) REVERT: A 746 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6926 (ttp-110) REVERT: A 775 GLU cc_start: 0.6689 (tt0) cc_final: 0.5877 (mt-10) REVERT: A 781 ASP cc_start: 0.6629 (m-30) cc_final: 0.6148 (m-30) REVERT: A 783 HIS cc_start: 0.6183 (m-70) cc_final: 0.5945 (m-70) REVERT: A 784 VAL cc_start: 0.5858 (m) cc_final: 0.5573 (p) REVERT: A 786 GLN cc_start: 0.7528 (tm-30) cc_final: 0.6707 (tm130) REVERT: A 823 GLN cc_start: 0.5830 (tt0) cc_final: 0.5279 (mm-40) REVERT: A 828 LYS cc_start: 0.6774 (mmmm) cc_final: 0.6262 (mttp) REVERT: A 851 ILE cc_start: 0.7249 (mm) cc_final: 0.6984 (mm) REVERT: A 857 GLN cc_start: 0.6864 (mt0) cc_final: 0.6015 (mm110) REVERT: A 858 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.5748 (tpp) REVERT: A 879 MET cc_start: 0.7332 (ttm) cc_final: 0.7032 (ttm) REVERT: A 881 LYS cc_start: 0.6146 (mttp) cc_final: 0.5455 (mmmt) REVERT: A 889 GLU cc_start: 0.6282 (tm-30) cc_final: 0.5635 (tp30) REVERT: A 983 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6276 (mt) REVERT: A 989 MET cc_start: 0.6181 (mmt) cc_final: 0.5752 (mmm) REVERT: A 1015 ASP cc_start: 0.5711 (m-30) cc_final: 0.5241 (m-30) REVERT: A 1061 LYS cc_start: 0.6929 (mtpm) cc_final: 0.6654 (mtpp) REVERT: A 1076 LEU cc_start: 0.6090 (tp) cc_final: 0.5641 (tm) REVERT: A 1083 ASN cc_start: 0.5875 (t0) cc_final: 0.5359 (m-40) REVERT: A 1123 THR cc_start: 0.6171 (t) cc_final: 0.5822 (t) REVERT: A 1125 GLN cc_start: 0.6734 (tp40) cc_final: 0.6373 (tp-100) REVERT: A 1332 TYR cc_start: 0.4898 (t80) cc_final: 0.4445 (t80) REVERT: A 1509 GLN cc_start: 0.5703 (tt0) cc_final: 0.5019 (tp-100) REVERT: A 1576 ASP cc_start: 0.5162 (p0) cc_final: 0.4889 (m-30) REVERT: A 1592 MET cc_start: 0.7297 (tpt) cc_final: 0.6493 (tpt) REVERT: A 1607 GLU cc_start: 0.6357 (mm-30) cc_final: 0.6058 (mm-30) REVERT: A 1627 LYS cc_start: 0.7076 (mmpt) cc_final: 0.6675 (mtmt) REVERT: A 1761 LEU cc_start: 0.5901 (mt) cc_final: 0.5655 (mp) REVERT: A 1762 MET cc_start: 0.4804 (mmp) cc_final: 0.4474 (mmp) REVERT: A 1768 ARG cc_start: 0.7194 (ptt90) cc_final: 0.6817 (ptt-90) REVERT: A 1775 GLU cc_start: 0.5816 (tt0) cc_final: 0.5116 (mt-10) REVERT: A 1795 VAL cc_start: 0.6114 (t) cc_final: 0.5736 (t) REVERT: A 1799 GLU cc_start: 0.5751 (mt-10) cc_final: 0.5334 (mt-10) REVERT: A 1829 TRP cc_start: 0.5549 (m100) cc_final: 0.5109 (m100) REVERT: A 1849 ASP cc_start: 0.6093 (t0) cc_final: 0.4992 (m-30) REVERT: A 1852 LYS cc_start: 0.5357 (mttp) cc_final: 0.5042 (mttp) REVERT: A 1917 LYS cc_start: 0.4738 (tppt) cc_final: 0.4416 (tppt) REVERT: A 1921 ASP cc_start: 0.5179 (m-30) cc_final: 0.4584 (p0) REVERT: A 1971 PRO cc_start: 0.3963 (Cg_endo) cc_final: 0.3696 (Cg_exo) REVERT: A 2042 GLN cc_start: 0.6170 (OUTLIER) cc_final: 0.5215 (tm-30) REVERT: A 2085 MET cc_start: 0.5995 (pmm) cc_final: 0.5678 (pmm) REVERT: A 2127 LYS cc_start: 0.6006 (mptt) cc_final: 0.5707 (mptt) REVERT: A 2162 LYS cc_start: 0.7596 (mttp) cc_final: 0.7295 (mmtm) REVERT: A 2170 GLN cc_start: 0.6284 (tt0) cc_final: 0.6081 (tt0) REVERT: A 2221 LYS cc_start: 0.5768 (tttm) cc_final: 0.5442 (ttmm) REVERT: A 2239 LYS cc_start: 0.6364 (tmmt) cc_final: 0.5837 (ttpt) REVERT: A 2243 GLU cc_start: 0.6346 (tm-30) cc_final: 0.5893 (pt0) REVERT: A 2292 CYS cc_start: 0.6701 (t) cc_final: 0.5758 (p) REVERT: A 2356 MET cc_start: 0.6241 (mtm) cc_final: 0.5930 (mtp) REVERT: A 2357 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6090 (mp0) REVERT: A 2369 LYS cc_start: 0.7786 (mttt) cc_final: 0.6582 (mmpt) REVERT: A 2414 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6604 (mm-40) REVERT: A 2427 ARG cc_start: 0.6933 (tpt90) cc_final: 0.6372 (tpm-80) REVERT: A 2428 ASP cc_start: 0.6109 (t70) cc_final: 0.5706 (t70) REVERT: A 2430 GLU cc_start: 0.6001 (mm-30) cc_final: 0.5669 (tt0) REVERT: A 2434 VAL cc_start: 0.6858 (t) cc_final: 0.6598 (p) REVERT: A 2447 LYS cc_start: 0.7767 (mmpt) cc_final: 0.7436 (mmpt) REVERT: A 2450 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7134 (tt0) REVERT: A 2498 ILE cc_start: 0.7058 (pt) cc_final: 0.6783 (pp) REVERT: A 2504 ASP cc_start: 0.5937 (m-30) cc_final: 0.5222 (m-30) REVERT: A 2522 ARG cc_start: 0.5573 (tmt170) cc_final: 0.5313 (ttm-80) REVERT: A 2551 GLU cc_start: 0.8020 (tt0) cc_final: 0.7568 (tt0) REVERT: A 2795 GLN cc_start: 0.6394 (tm-30) cc_final: 0.6108 (tp40) REVERT: A 2818 LYS cc_start: 0.7590 (tttt) cc_final: 0.6772 (tttm) REVERT: A 2839 ASP cc_start: 0.5729 (m-30) cc_final: 0.5342 (m-30) REVERT: A 2864 GLN cc_start: 0.7091 (mm-40) cc_final: 0.5952 (tm-30) REVERT: A 2935 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6226 (mm-30) REVERT: A 2954 GLN cc_start: 0.6730 (tt0) cc_final: 0.6517 (tt0) REVERT: A 2978 LYS cc_start: 0.5755 (tttt) cc_final: 0.5549 (tttt) REVERT: A 3007 GLU cc_start: 0.7094 (mp0) cc_final: 0.6030 (mm-30) REVERT: A 3090 TYR cc_start: 0.7492 (m-80) cc_final: 0.6358 (m-80) REVERT: A 3140 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6721 (mt-10) REVERT: A 3158 LYS cc_start: 0.6649 (mtpp) cc_final: 0.6278 (mtpt) REVERT: A 3172 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7376 (ttmt) REVERT: A 3173 MET cc_start: 0.7339 (mmm) cc_final: 0.6830 (tpp) REVERT: A 3191 SER cc_start: 0.7440 (t) cc_final: 0.7200 (m) REVERT: A 3237 SER cc_start: 0.7230 (t) cc_final: 0.6958 (m) REVERT: A 3238 MET cc_start: 0.7696 (mtm) cc_final: 0.7083 (mtp) REVERT: A 3284 SER cc_start: 0.7696 (p) cc_final: 0.7435 (p) REVERT: A 3287 ARG cc_start: 0.6687 (ptm160) cc_final: 0.6218 (ptm-80) REVERT: A 3289 ARG cc_start: 0.6659 (mpt90) cc_final: 0.6005 (mpt-90) REVERT: A 3327 ASN cc_start: 0.5786 (m-40) cc_final: 0.4972 (m110) REVERT: A 3387 GLU cc_start: 0.6077 (tp30) cc_final: 0.5605 (tt0) REVERT: A 3582 GLU cc_start: 0.5890 (mp0) cc_final: 0.5558 (mt-10) REVERT: A 3654 MET cc_start: -0.4596 (OUTLIER) cc_final: -0.5122 (tmm) REVERT: A 3718 ARG cc_start: 0.5521 (mpp80) cc_final: 0.5180 (mpp80) REVERT: A 3734 ARG cc_start: 0.6142 (tpp80) cc_final: 0.5862 (ttm170) REVERT: A 3747 GLU cc_start: 0.6923 (tt0) cc_final: 0.6697 (tt0) REVERT: A 3772 ASN cc_start: 0.7161 (p0) cc_final: 0.6562 (p0) REVERT: A 3796 MET cc_start: 0.7997 (mmp) cc_final: 0.7571 (mmm) REVERT: A 3863 ASN cc_start: 0.6054 (p0) cc_final: 0.5791 (p0) REVERT: A 3869 THR cc_start: 0.6367 (m) cc_final: 0.6026 (m) REVERT: A 3877 LYS cc_start: 0.7323 (mtmm) cc_final: 0.6902 (tptp) REVERT: A 3932 MET cc_start: 0.7525 (mmm) cc_final: 0.7025 (mmm) REVERT: A 4082 ARG cc_start: 0.4948 (ttm110) cc_final: 0.4713 (ttm-80) REVERT: A 4085 LYS cc_start: 0.6462 (tptp) cc_final: 0.6194 (tptp) REVERT: A 4108 MET cc_start: 0.7588 (ttm) cc_final: 0.7299 (mtt) REVERT: B 48 MET cc_start: 0.6232 (mtt) cc_final: 0.5829 (mtp) REVERT: B 78 SER cc_start: 0.7970 (m) cc_final: 0.7637 (m) REVERT: B 160 LYS cc_start: 0.7461 (tppp) cc_final: 0.6910 (tmtt) REVERT: B 161 MET cc_start: 0.8587 (mtm) cc_final: 0.8339 (mtt) REVERT: B 165 ARG cc_start: 0.6785 (ttp-110) cc_final: 0.6023 (mtp85) REVERT: B 192 ASP cc_start: 0.5556 (t70) cc_final: 0.5246 (t70) REVERT: B 294 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6221 (mt-10) REVERT: B 333 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6532 (mt-10) REVERT: B 335 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6764 (tt0) REVERT: B 393 GLU cc_start: 0.5872 (mp0) cc_final: 0.5307 (tt0) REVERT: B 409 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.5446 (t80) REVERT: B 443 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5509 (mtmt) REVERT: C 40 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.4227 (tmm) REVERT: C 84 MET cc_start: 0.3756 (pmt) cc_final: 0.3480 (pmm) REVERT: C 92 GLU cc_start: 0.5944 (pp20) cc_final: 0.5541 (pm20) REVERT: C 210 MET cc_start: 0.5714 (ppp) cc_final: 0.4968 (tpt) REVERT: C 233 LYS cc_start: 0.4035 (mttt) cc_final: 0.3180 (mmtt) REVERT: C 271 ARG cc_start: 0.6689 (mtt-85) cc_final: 0.6408 (ptp-110) REVERT: C 275 THR cc_start: 0.7650 (p) cc_final: 0.7181 (t) REVERT: C 286 LYS cc_start: 0.6583 (ttpt) cc_final: 0.6113 (ttpp) REVERT: C 287 GLU cc_start: 0.7279 (mp0) cc_final: 0.6704 (mp0) REVERT: C 288 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6219 (m-30) REVERT: C 302 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5702 (mt-10) REVERT: C 304 GLU cc_start: 0.7119 (tt0) cc_final: 0.6917 (tt0) REVERT: C 315 ARG cc_start: 0.6727 (tpp-160) cc_final: 0.6247 (tpp80) REVERT: C 332 LYS cc_start: 0.7198 (ptmt) cc_final: 0.6784 (ptmm) REVERT: C 336 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6348 (pp20) REVERT: C 343 LEU cc_start: 0.8168 (mt) cc_final: 0.7863 (mp) REVERT: C 371 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6267 (pp20) REVERT: C 409 PHE cc_start: 0.5314 (m-80) cc_final: 0.5088 (m-80) REVERT: C 427 MET cc_start: 0.7510 (ppp) cc_final: 0.6921 (pp-130) REVERT: C 430 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7986 (pp) REVERT: C 474 GLU cc_start: 0.6417 (tm-30) cc_final: 0.6073 (tm-30) REVERT: C 481 LYS cc_start: 0.6472 (tptt) cc_final: 0.6205 (tptm) REVERT: C 488 GLN cc_start: 0.5608 (OUTLIER) cc_final: 0.5148 (tp-100) REVERT: C 552 GLU cc_start: 0.7070 (pt0) cc_final: 0.6394 (pp20) REVERT: C 731 MET cc_start: 0.3914 (ptt) cc_final: 0.3439 (ptp) outliers start: 112 outliers final: 44 residues processed: 771 average time/residue: 1.4954 time to fit residues: 1420.9102 Evaluate side-chains 724 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 663 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain A residue 1681 ASP Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3227 ILE Chi-restraints excluded: chain A residue 3262 LEU Chi-restraints excluded: chain A residue 3270 ASP Chi-restraints excluded: chain A residue 3326 GLN Chi-restraints excluded: chain A residue 3330 LEU Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3654 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 488 GLN Chi-restraints excluded: chain C residue 536 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 392 optimal weight: 0.0010 chunk 267 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 chunk 194 optimal weight: 0.0980 chunk 401 optimal weight: 0.7980 chunk 325 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 422 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 533 HIS A1457 GLN A1716 GLN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2275 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3154 GLN ** A3296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3524 ASN A3924 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN C 411 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40414 Z= 0.229 Angle : 0.682 13.734 54841 Z= 0.342 Chirality : 0.042 0.191 6243 Planarity : 0.005 0.060 6791 Dihedral : 12.208 172.775 5773 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.79 % Favored : 90.19 % Rotamer: Outliers : 3.12 % Allowed : 18.83 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 4795 helix: 0.53 (0.10), residues: 2847 sheet: -0.90 (0.36), residues: 200 loop : -2.72 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2196 HIS 0.006 0.001 HIS A1367 PHE 0.029 0.002 PHE A2260 TYR 0.025 0.002 TYR A3442 ARG 0.015 0.001 ARG A1735 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 687 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6543 (mpt90) REVERT: A 80 GLU cc_start: 0.6279 (mp0) cc_final: 0.5922 (mp0) REVERT: A 146 GLU cc_start: 0.6059 (tp30) cc_final: 0.5621 (tm-30) REVERT: A 165 LYS cc_start: 0.5091 (OUTLIER) cc_final: 0.4386 (tttm) REVERT: A 172 GLU cc_start: 0.7864 (tt0) cc_final: 0.6760 (tm-30) REVERT: A 191 ASN cc_start: 0.7761 (m-40) cc_final: 0.7416 (m110) REVERT: A 239 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6651 (mp0) REVERT: A 243 GLN cc_start: 0.6083 (tp40) cc_final: 0.5394 (mp10) REVERT: A 263 LYS cc_start: 0.7191 (mptt) cc_final: 0.6521 (mppt) REVERT: A 307 GLU cc_start: 0.6875 (tt0) cc_final: 0.6635 (tt0) REVERT: A 329 LYS cc_start: 0.6848 (mtmp) cc_final: 0.6532 (mtmm) REVERT: A 340 TYR cc_start: 0.6666 (t80) cc_final: 0.6226 (t80) REVERT: A 342 MET cc_start: 0.6576 (mmt) cc_final: 0.6245 (mmt) REVERT: A 373 CYS cc_start: 0.6992 (m) cc_final: 0.6558 (m) REVERT: A 379 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5838 (mtpm) REVERT: A 380 ASP cc_start: 0.4052 (OUTLIER) cc_final: 0.3259 (m-30) REVERT: A 395 MET cc_start: 0.6180 (ptm) cc_final: 0.5706 (ptm) REVERT: A 415 GLN cc_start: 0.6033 (OUTLIER) cc_final: 0.5633 (tp40) REVERT: A 423 TYR cc_start: 0.7234 (m-80) cc_final: 0.6372 (m-80) REVERT: A 441 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5796 (ttt) REVERT: A 476 ARG cc_start: 0.6551 (mtp-110) cc_final: 0.6340 (mtp-110) REVERT: A 524 TYR cc_start: 0.6975 (p90) cc_final: 0.6749 (p90) REVERT: A 578 LYS cc_start: 0.7027 (ptpt) cc_final: 0.6541 (ptpp) REVERT: A 659 ARG cc_start: 0.6651 (ptt90) cc_final: 0.5327 (ptp-110) REVERT: A 662 LEU cc_start: 0.7471 (mp) cc_final: 0.7249 (mm) REVERT: A 669 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6772 (mp) REVERT: A 746 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6925 (ttp-110) REVERT: A 775 GLU cc_start: 0.6705 (tt0) cc_final: 0.5895 (mt-10) REVERT: A 781 ASP cc_start: 0.6648 (m-30) cc_final: 0.6152 (m-30) REVERT: A 783 HIS cc_start: 0.6342 (m-70) cc_final: 0.6101 (m-70) REVERT: A 784 VAL cc_start: 0.5894 (m) cc_final: 0.5591 (p) REVERT: A 786 GLN cc_start: 0.7522 (tm-30) cc_final: 0.6695 (tm130) REVERT: A 823 GLN cc_start: 0.5836 (tt0) cc_final: 0.5265 (mm-40) REVERT: A 828 LYS cc_start: 0.6771 (mmmm) cc_final: 0.6296 (mttp) REVERT: A 851 ILE cc_start: 0.7226 (mm) cc_final: 0.6950 (mm) REVERT: A 857 GLN cc_start: 0.6900 (mt0) cc_final: 0.6059 (mm110) REVERT: A 879 MET cc_start: 0.7360 (ttm) cc_final: 0.7101 (ttm) REVERT: A 881 LYS cc_start: 0.6177 (mttp) cc_final: 0.5470 (mmmt) REVERT: A 889 GLU cc_start: 0.6296 (tm-30) cc_final: 0.5643 (tp30) REVERT: A 925 GLN cc_start: 0.5900 (mm-40) cc_final: 0.5635 (tp-100) REVERT: A 937 MET cc_start: 0.7530 (mtt) cc_final: 0.7215 (mtt) REVERT: A 939 MET cc_start: 0.7496 (mmm) cc_final: 0.7183 (mmp) REVERT: A 983 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6440 (mt) REVERT: A 989 MET cc_start: 0.6015 (mmt) cc_final: 0.5733 (mmm) REVERT: A 990 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: A 1015 ASP cc_start: 0.5686 (m-30) cc_final: 0.5257 (m-30) REVERT: A 1043 GLN cc_start: 0.6180 (mt0) cc_final: 0.5782 (mt0) REVERT: A 1061 LYS cc_start: 0.6912 (mtpm) cc_final: 0.6634 (mtpp) REVERT: A 1076 LEU cc_start: 0.6100 (tp) cc_final: 0.5692 (tm) REVERT: A 1083 ASN cc_start: 0.5859 (t0) cc_final: 0.5369 (m-40) REVERT: A 1123 THR cc_start: 0.6163 (t) cc_final: 0.5788 (t) REVERT: A 1125 GLN cc_start: 0.6745 (tp40) cc_final: 0.6457 (tp-100) REVERT: A 1332 TYR cc_start: 0.4918 (t80) cc_final: 0.4508 (t80) REVERT: A 1392 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6951 (mmm) REVERT: A 1509 GLN cc_start: 0.5733 (tt0) cc_final: 0.5028 (tp-100) REVERT: A 1576 ASP cc_start: 0.5232 (p0) cc_final: 0.4937 (m-30) REVERT: A 1607 GLU cc_start: 0.6385 (mm-30) cc_final: 0.6098 (mm-30) REVERT: A 1627 LYS cc_start: 0.7084 (mmpt) cc_final: 0.6674 (mtmt) REVERT: A 1735 ARG cc_start: 0.5603 (mtm-85) cc_final: 0.5132 (ptm160) REVERT: A 1761 LEU cc_start: 0.5845 (mt) cc_final: 0.5612 (mp) REVERT: A 1762 MET cc_start: 0.4786 (mmp) cc_final: 0.4514 (mmp) REVERT: A 1775 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5237 (mt-10) REVERT: A 1795 VAL cc_start: 0.6172 (t) cc_final: 0.5769 (t) REVERT: A 1799 GLU cc_start: 0.5737 (mt-10) cc_final: 0.5294 (mt-10) REVERT: A 1849 ASP cc_start: 0.6105 (t0) cc_final: 0.5004 (m-30) REVERT: A 1917 LYS cc_start: 0.4689 (tppt) cc_final: 0.4376 (tppt) REVERT: A 1921 ASP cc_start: 0.5214 (m-30) cc_final: 0.4583 (p0) REVERT: A 1971 PRO cc_start: 0.4009 (Cg_endo) cc_final: 0.3790 (Cg_exo) REVERT: A 2042 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5288 (tm-30) REVERT: A 2085 MET cc_start: 0.5928 (pmm) cc_final: 0.5679 (pmm) REVERT: A 2127 LYS cc_start: 0.6133 (mptt) cc_final: 0.5677 (mptt) REVERT: A 2162 LYS cc_start: 0.7590 (mttp) cc_final: 0.7294 (mmtm) REVERT: A 2170 GLN cc_start: 0.6297 (tt0) cc_final: 0.6029 (tt0) REVERT: A 2221 LYS cc_start: 0.5879 (tttm) cc_final: 0.5562 (ttmm) REVERT: A 2227 LYS cc_start: 0.5957 (tptt) cc_final: 0.5755 (tppp) REVERT: A 2239 LYS cc_start: 0.6297 (tmmt) cc_final: 0.5840 (ttpt) REVERT: A 2243 GLU cc_start: 0.6353 (tm-30) cc_final: 0.5864 (pt0) REVERT: A 2292 CYS cc_start: 0.6651 (t) cc_final: 0.5780 (p) REVERT: A 2352 HIS cc_start: 0.7425 (m90) cc_final: 0.7185 (m-70) REVERT: A 2356 MET cc_start: 0.6318 (mtm) cc_final: 0.6092 (mtp) REVERT: A 2357 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6371 (mp0) REVERT: A 2362 VAL cc_start: 0.7658 (t) cc_final: 0.7276 (m) REVERT: A 2369 LYS cc_start: 0.7790 (mttt) cc_final: 0.6577 (mmpt) REVERT: A 2414 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6576 (mm-40) REVERT: A 2427 ARG cc_start: 0.6897 (tpt90) cc_final: 0.6360 (tpm-80) REVERT: A 2428 ASP cc_start: 0.6256 (t70) cc_final: 0.5819 (t70) REVERT: A 2430 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5676 (tt0) REVERT: A 2434 VAL cc_start: 0.6912 (t) cc_final: 0.6661 (p) REVERT: A 2447 LYS cc_start: 0.7766 (mmpt) cc_final: 0.7403 (mmpt) REVERT: A 2450 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7138 (tt0) REVERT: A 2498 ILE cc_start: 0.7183 (pt) cc_final: 0.6900 (pp) REVERT: A 2504 ASP cc_start: 0.5972 (m-30) cc_final: 0.5258 (m-30) REVERT: A 2522 ARG cc_start: 0.5626 (tmt170) cc_final: 0.5277 (ttm-80) REVERT: A 2537 ASP cc_start: 0.5933 (m-30) cc_final: 0.5563 (m-30) REVERT: A 2551 GLU cc_start: 0.8076 (tt0) cc_final: 0.7605 (tt0) REVERT: A 2795 GLN cc_start: 0.6549 (tm-30) cc_final: 0.6175 (tp40) REVERT: A 2818 LYS cc_start: 0.7534 (tttt) cc_final: 0.6764 (tttm) REVERT: A 2839 ASP cc_start: 0.5735 (m-30) cc_final: 0.5337 (m-30) REVERT: A 2864 GLN cc_start: 0.7103 (mm-40) cc_final: 0.5960 (tm-30) REVERT: A 2935 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6556 (mm-30) REVERT: A 2954 GLN cc_start: 0.6785 (tt0) cc_final: 0.6474 (tt0) REVERT: A 3007 GLU cc_start: 0.7047 (mp0) cc_final: 0.6191 (mm-30) REVERT: A 3067 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6073 (tttp) REVERT: A 3090 TYR cc_start: 0.7469 (m-80) cc_final: 0.6428 (m-80) REVERT: A 3140 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6507 (mt-10) REVERT: A 3158 LYS cc_start: 0.6623 (mtpp) cc_final: 0.6345 (mtpt) REVERT: A 3173 MET cc_start: 0.7199 (mmm) cc_final: 0.6787 (mpp) REVERT: A 3191 SER cc_start: 0.7471 (t) cc_final: 0.7212 (m) REVERT: A 3237 SER cc_start: 0.7201 (t) cc_final: 0.6927 (m) REVERT: A 3238 MET cc_start: 0.7823 (mtm) cc_final: 0.7157 (mtp) REVERT: A 3270 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5775 (t0) REVERT: A 3284 SER cc_start: 0.7746 (p) cc_final: 0.7454 (p) REVERT: A 3287 ARG cc_start: 0.6634 (ptm160) cc_final: 0.6061 (ptt90) REVERT: A 3289 ARG cc_start: 0.6616 (mpt90) cc_final: 0.6019 (mpt-90) REVERT: A 3327 ASN cc_start: 0.5740 (m-40) cc_final: 0.4874 (m110) REVERT: A 3387 GLU cc_start: 0.6150 (tp30) cc_final: 0.5679 (tt0) REVERT: A 3500 SER cc_start: 0.6794 (t) cc_final: 0.6505 (m) REVERT: A 3582 GLU cc_start: 0.5916 (mp0) cc_final: 0.5681 (mt-10) REVERT: A 3718 ARG cc_start: 0.5483 (mpp80) cc_final: 0.5148 (mpp80) REVERT: A 3734 ARG cc_start: 0.6188 (tpp80) cc_final: 0.5236 (tpp-160) REVERT: A 3747 GLU cc_start: 0.7151 (tt0) cc_final: 0.6901 (tt0) REVERT: A 3772 ASN cc_start: 0.7047 (p0) cc_final: 0.6409 (p0) REVERT: A 3796 MET cc_start: 0.8051 (mmp) cc_final: 0.7345 (mmm) REVERT: A 3863 ASN cc_start: 0.6109 (p0) cc_final: 0.5845 (p0) REVERT: A 3869 THR cc_start: 0.6294 (m) cc_final: 0.5957 (m) REVERT: A 3877 LYS cc_start: 0.7337 (mtmm) cc_final: 0.6917 (tptp) REVERT: A 4098 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6550 (mp) REVERT: A 4108 MET cc_start: 0.7602 (ttm) cc_final: 0.7295 (mtt) REVERT: B 160 LYS cc_start: 0.7442 (tppp) cc_final: 0.6832 (tmtt) REVERT: B 161 MET cc_start: 0.8549 (mtm) cc_final: 0.8327 (mtt) REVERT: B 165 ARG cc_start: 0.6825 (ttp-110) cc_final: 0.6046 (mtp85) REVERT: B 192 ASP cc_start: 0.5551 (t70) cc_final: 0.5170 (t70) REVERT: B 294 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6240 (mt-10) REVERT: B 317 LYS cc_start: 0.5793 (mttt) cc_final: 0.5362 (mmmt) REVERT: B 333 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6520 (mt-10) REVERT: B 335 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6773 (tt0) REVERT: B 347 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7246 (mt) REVERT: B 393 GLU cc_start: 0.5913 (mp0) cc_final: 0.5308 (tt0) REVERT: B 409 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.5600 (t80) REVERT: B 443 LYS cc_start: 0.5993 (OUTLIER) cc_final: 0.5585 (mtmt) REVERT: C 20 MET cc_start: 0.3340 (OUTLIER) cc_final: 0.1867 (tpp) REVERT: C 84 MET cc_start: 0.3600 (pmt) cc_final: 0.3344 (pmm) REVERT: C 210 MET cc_start: 0.5866 (ppp) cc_final: 0.5093 (tpt) REVERT: C 233 LYS cc_start: 0.4110 (mttt) cc_final: 0.3202 (mmtt) REVERT: C 271 ARG cc_start: 0.6613 (mtt-85) cc_final: 0.6319 (ptp-110) REVERT: C 286 LYS cc_start: 0.6620 (ttpt) cc_final: 0.6135 (ttpp) REVERT: C 287 GLU cc_start: 0.7262 (mp0) cc_final: 0.6744 (mp0) REVERT: C 288 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6209 (m-30) REVERT: C 302 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5678 (mt-10) REVERT: C 304 GLU cc_start: 0.7177 (tt0) cc_final: 0.6895 (tt0) REVERT: C 311 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6799 (tt) REVERT: C 315 ARG cc_start: 0.6826 (tpp-160) cc_final: 0.6306 (tpp80) REVERT: C 336 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6400 (pp20) REVERT: C 343 LEU cc_start: 0.8112 (mt) cc_final: 0.7804 (mp) REVERT: C 371 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6293 (pp20) REVERT: C 409 PHE cc_start: 0.5396 (m-80) cc_final: 0.5177 (m-80) REVERT: C 427 MET cc_start: 0.7706 (ppp) cc_final: 0.7010 (pp-130) REVERT: C 430 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (pp) REVERT: C 474 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6156 (tm-30) REVERT: C 481 LYS cc_start: 0.6577 (tptt) cc_final: 0.6284 (tptm) REVERT: C 482 ILE cc_start: 0.6465 (pt) cc_final: 0.5862 (pt) REVERT: C 552 GLU cc_start: 0.7067 (pt0) cc_final: 0.6405 (pp20) REVERT: C 731 MET cc_start: 0.3916 (ptt) cc_final: 0.3444 (ptp) outliers start: 129 outliers final: 58 residues processed: 756 average time/residue: 1.5345 time to fit residues: 1426.4062 Evaluate side-chains 745 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 663 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1057 LYS Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1485 SER Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2995 GLU Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3262 LEU Chi-restraints excluded: chain A residue 3270 ASP Chi-restraints excluded: chain A residue 3302 LYS Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 158 optimal weight: 1.9990 chunk 423 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 471 optimal weight: 3.9990 chunk 391 optimal weight: 0.9990 chunk 218 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 155 optimal weight: 0.3980 chunk 247 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 415 GLN A 533 HIS ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3166 ASN ** A3296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3524 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 411 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40414 Z= 0.236 Angle : 0.679 12.731 54841 Z= 0.340 Chirality : 0.042 0.187 6243 Planarity : 0.005 0.059 6791 Dihedral : 12.200 175.286 5773 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.75 % Favored : 90.23 % Rotamer: Outliers : 3.40 % Allowed : 19.21 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.12), residues: 4795 helix: 0.56 (0.10), residues: 2850 sheet: -0.84 (0.36), residues: 202 loop : -2.70 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2196 HIS 0.010 0.001 HIS A1367 PHE 0.030 0.002 PHE A2260 TYR 0.028 0.002 TYR A3442 ARG 0.014 0.001 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 690 time to evaluate : 4.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6893 (mmt180) cc_final: 0.6576 (mpt90) REVERT: A 80 GLU cc_start: 0.6294 (mp0) cc_final: 0.5932 (mp0) REVERT: A 143 LEU cc_start: 0.7006 (mt) cc_final: 0.6558 (mt) REVERT: A 146 GLU cc_start: 0.6097 (tp30) cc_final: 0.5886 (mm-30) REVERT: A 172 GLU cc_start: 0.7856 (tt0) cc_final: 0.6766 (tm-30) REVERT: A 191 ASN cc_start: 0.7764 (m-40) cc_final: 0.7421 (m110) REVERT: A 243 GLN cc_start: 0.6411 (tp40) cc_final: 0.5638 (mp10) REVERT: A 263 LYS cc_start: 0.7188 (mptt) cc_final: 0.6567 (mppt) REVERT: A 326 MET cc_start: 0.6016 (mtp) cc_final: 0.5475 (mtm) REVERT: A 329 LYS cc_start: 0.6821 (mtmp) cc_final: 0.6447 (mtmm) REVERT: A 340 TYR cc_start: 0.6776 (t80) cc_final: 0.6342 (t80) REVERT: A 342 MET cc_start: 0.6241 (mmt) cc_final: 0.5988 (mmt) REVERT: A 373 CYS cc_start: 0.6789 (m) cc_final: 0.6392 (m) REVERT: A 379 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.5904 (mtpm) REVERT: A 380 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.4621 (m-30) REVERT: A 395 MET cc_start: 0.6229 (ptm) cc_final: 0.5679 (ptm) REVERT: A 423 TYR cc_start: 0.7271 (m-80) cc_final: 0.6462 (m-80) REVERT: A 453 MET cc_start: 0.6608 (tpp) cc_final: 0.6112 (tpp) REVERT: A 476 ARG cc_start: 0.6487 (mtp-110) cc_final: 0.6268 (mtp-110) REVERT: A 524 TYR cc_start: 0.6919 (p90) cc_final: 0.6696 (p90) REVERT: A 578 LYS cc_start: 0.6983 (ptpt) cc_final: 0.6499 (ptpp) REVERT: A 631 ARG cc_start: 0.5251 (ttm110) cc_final: 0.4977 (mtp-110) REVERT: A 659 ARG cc_start: 0.6863 (ptt90) cc_final: 0.5602 (ptp-110) REVERT: A 662 LEU cc_start: 0.7653 (mp) cc_final: 0.7422 (mm) REVERT: A 669 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6842 (mp) REVERT: A 746 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6915 (ttp-110) REVERT: A 767 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6681 (tt0) REVERT: A 775 GLU cc_start: 0.6684 (tt0) cc_final: 0.5956 (mp0) REVERT: A 781 ASP cc_start: 0.6678 (m-30) cc_final: 0.6174 (m-30) REVERT: A 783 HIS cc_start: 0.6387 (m-70) cc_final: 0.6121 (m-70) REVERT: A 784 VAL cc_start: 0.5908 (m) cc_final: 0.5591 (p) REVERT: A 786 GLN cc_start: 0.7502 (tm-30) cc_final: 0.6706 (tm130) REVERT: A 823 GLN cc_start: 0.5777 (tt0) cc_final: 0.5228 (mm-40) REVERT: A 828 LYS cc_start: 0.6739 (mmmm) cc_final: 0.6321 (mttp) REVERT: A 851 ILE cc_start: 0.7214 (mm) cc_final: 0.6972 (mm) REVERT: A 857 GLN cc_start: 0.7024 (mt0) cc_final: 0.6127 (mm110) REVERT: A 879 MET cc_start: 0.7421 (ttm) cc_final: 0.7161 (ttm) REVERT: A 881 LYS cc_start: 0.6218 (mttp) cc_final: 0.5503 (mmmt) REVERT: A 889 GLU cc_start: 0.6354 (tm-30) cc_final: 0.5735 (tp30) REVERT: A 900 GLU cc_start: 0.4539 (tm-30) cc_final: 0.4313 (tm-30) REVERT: A 983 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6343 (mt) REVERT: A 989 MET cc_start: 0.5979 (mmt) cc_final: 0.5613 (mmm) REVERT: A 990 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6137 (pm20) REVERT: A 1015 ASP cc_start: 0.5971 (m-30) cc_final: 0.5585 (m-30) REVERT: A 1061 LYS cc_start: 0.6918 (mtpm) cc_final: 0.6553 (mtpp) REVERT: A 1076 LEU cc_start: 0.6035 (tp) cc_final: 0.5704 (tm) REVERT: A 1083 ASN cc_start: 0.6171 (t0) cc_final: 0.5686 (m-40) REVERT: A 1123 THR cc_start: 0.6160 (t) cc_final: 0.5716 (t) REVERT: A 1125 GLN cc_start: 0.6757 (tp40) cc_final: 0.6468 (tp-100) REVERT: A 1136 ARG cc_start: 0.4982 (ptp90) cc_final: 0.4688 (mtm110) REVERT: A 1332 TYR cc_start: 0.4923 (t80) cc_final: 0.4494 (t80) REVERT: A 1392 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6919 (mmm) REVERT: A 1509 GLN cc_start: 0.5753 (tt0) cc_final: 0.5046 (tp-100) REVERT: A 1576 ASP cc_start: 0.5282 (p0) cc_final: 0.4948 (m-30) REVERT: A 1607 GLU cc_start: 0.6341 (mm-30) cc_final: 0.6045 (mm-30) REVERT: A 1627 LYS cc_start: 0.7116 (mmpt) cc_final: 0.6693 (mtmt) REVERT: A 1735 ARG cc_start: 0.5701 (mtm-85) cc_final: 0.5348 (ptm160) REVERT: A 1762 MET cc_start: 0.4692 (mmp) cc_final: 0.4354 (mmp) REVERT: A 1775 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5546 (mt-10) REVERT: A 1784 ARG cc_start: 0.5222 (mpp80) cc_final: 0.4522 (mtm110) REVERT: A 1795 VAL cc_start: 0.6409 (t) cc_final: 0.5987 (t) REVERT: A 1799 GLU cc_start: 0.5755 (mt-10) cc_final: 0.5310 (mt-10) REVERT: A 1849 ASP cc_start: 0.6074 (t0) cc_final: 0.4973 (m-30) REVERT: A 1852 LYS cc_start: 0.5741 (mttm) cc_final: 0.5488 (mttp) REVERT: A 1971 PRO cc_start: 0.4011 (Cg_endo) cc_final: 0.3794 (Cg_exo) REVERT: A 2042 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5308 (tm-30) REVERT: A 2085 MET cc_start: 0.6213 (pmm) cc_final: 0.5784 (pmm) REVERT: A 2126 MET cc_start: 0.5770 (mtt) cc_final: 0.5469 (mtt) REVERT: A 2127 LYS cc_start: 0.6278 (mptt) cc_final: 0.5775 (mptt) REVERT: A 2162 LYS cc_start: 0.7607 (mttp) cc_final: 0.7322 (mmtm) REVERT: A 2170 GLN cc_start: 0.6162 (tt0) cc_final: 0.5896 (tt0) REVERT: A 2221 LYS cc_start: 0.5963 (tttm) cc_final: 0.5638 (ttmm) REVERT: A 2227 LYS cc_start: 0.5867 (tptt) cc_final: 0.5639 (tppp) REVERT: A 2239 LYS cc_start: 0.6272 (tmmt) cc_final: 0.5817 (ttpt) REVERT: A 2243 GLU cc_start: 0.6583 (tm-30) cc_final: 0.6106 (pt0) REVERT: A 2292 CYS cc_start: 0.6619 (t) cc_final: 0.5762 (p) REVERT: A 2356 MET cc_start: 0.6207 (mtm) cc_final: 0.5882 (mtp) REVERT: A 2357 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6267 (mp0) REVERT: A 2369 LYS cc_start: 0.7834 (mttt) cc_final: 0.6588 (mmpt) REVERT: A 2427 ARG cc_start: 0.6879 (tpt90) cc_final: 0.6333 (tpm-80) REVERT: A 2430 GLU cc_start: 0.6025 (mm-30) cc_final: 0.5696 (tt0) REVERT: A 2434 VAL cc_start: 0.6987 (t) cc_final: 0.6677 (p) REVERT: A 2447 LYS cc_start: 0.7775 (mmpt) cc_final: 0.7407 (mmpt) REVERT: A 2450 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7147 (tt0) REVERT: A 2498 ILE cc_start: 0.7117 (pt) cc_final: 0.6818 (pp) REVERT: A 2504 ASP cc_start: 0.6006 (m-30) cc_final: 0.5318 (m-30) REVERT: A 2522 ARG cc_start: 0.5555 (tmt170) cc_final: 0.5239 (ttm-80) REVERT: A 2551 GLU cc_start: 0.8057 (tt0) cc_final: 0.7627 (tt0) REVERT: A 2795 GLN cc_start: 0.6527 (tm-30) cc_final: 0.6176 (tp40) REVERT: A 2818 LYS cc_start: 0.7508 (tttt) cc_final: 0.6782 (tttm) REVERT: A 2839 ASP cc_start: 0.5755 (m-30) cc_final: 0.5342 (m-30) REVERT: A 2864 GLN cc_start: 0.7086 (mm-40) cc_final: 0.5950 (tm-30) REVERT: A 2935 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6539 (mm-30) REVERT: A 3007 GLU cc_start: 0.7226 (mp0) cc_final: 0.6300 (mm-30) REVERT: A 3067 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6067 (tttp) REVERT: A 3090 TYR cc_start: 0.7452 (m-80) cc_final: 0.6427 (m-80) REVERT: A 3140 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6569 (mt-10) REVERT: A 3158 LYS cc_start: 0.6631 (mtpp) cc_final: 0.6334 (mtpt) REVERT: A 3159 ARG cc_start: 0.5655 (ttp-110) cc_final: 0.5296 (ttp-110) REVERT: A 3166 ASN cc_start: 0.7330 (m-40) cc_final: 0.7050 (m110) REVERT: A 3172 LYS cc_start: 0.7611 (ttmm) cc_final: 0.5913 (tptp) REVERT: A 3173 MET cc_start: 0.7096 (mmm) cc_final: 0.6618 (mpp) REVERT: A 3191 SER cc_start: 0.7519 (t) cc_final: 0.7240 (m) REVERT: A 3237 SER cc_start: 0.7541 (t) cc_final: 0.7320 (m) REVERT: A 3284 SER cc_start: 0.7729 (p) cc_final: 0.7434 (p) REVERT: A 3287 ARG cc_start: 0.6670 (ptm160) cc_final: 0.6212 (ptm-80) REVERT: A 3289 ARG cc_start: 0.6663 (mpt90) cc_final: 0.6034 (mpt-90) REVERT: A 3327 ASN cc_start: 0.5777 (m-40) cc_final: 0.5221 (m110) REVERT: A 3387 GLU cc_start: 0.6217 (tp30) cc_final: 0.5705 (tt0) REVERT: A 3718 ARG cc_start: 0.5490 (mpp80) cc_final: 0.5134 (mpp80) REVERT: A 3734 ARG cc_start: 0.6179 (tpp80) cc_final: 0.5282 (tpp-160) REVERT: A 3747 GLU cc_start: 0.7082 (tt0) cc_final: 0.6857 (tt0) REVERT: A 3772 ASN cc_start: 0.6968 (p0) cc_final: 0.6341 (p0) REVERT: A 3796 MET cc_start: 0.8061 (mmp) cc_final: 0.7306 (mmm) REVERT: A 3863 ASN cc_start: 0.6267 (p0) cc_final: 0.6033 (p0) REVERT: A 3869 THR cc_start: 0.6303 (m) cc_final: 0.6038 (m) REVERT: A 3877 LYS cc_start: 0.7234 (mtmm) cc_final: 0.6810 (tptp) REVERT: A 3932 MET cc_start: 0.7613 (mmm) cc_final: 0.7146 (mmm) REVERT: A 3974 MET cc_start: 0.7416 (mtm) cc_final: 0.7185 (mpt) REVERT: A 4089 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.5946 (pt) REVERT: A 4098 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6527 (mp) REVERT: A 4108 MET cc_start: 0.7602 (ttm) cc_final: 0.7317 (mtt) REVERT: B 78 SER cc_start: 0.7912 (m) cc_final: 0.7653 (m) REVERT: B 160 LYS cc_start: 0.7450 (tppp) cc_final: 0.6862 (tmtt) REVERT: B 161 MET cc_start: 0.8510 (mtm) cc_final: 0.8282 (mtt) REVERT: B 165 ARG cc_start: 0.6784 (ttp-110) cc_final: 0.6029 (mtp85) REVERT: B 187 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6690 (mtm110) REVERT: B 192 ASP cc_start: 0.5515 (t70) cc_final: 0.5128 (t70) REVERT: B 258 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6367 (mtp85) REVERT: B 281 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7016 (pp) REVERT: B 294 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6249 (mt-10) REVERT: B 317 LYS cc_start: 0.5775 (mttt) cc_final: 0.5336 (mmmt) REVERT: B 333 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6694 (mt-10) REVERT: B 335 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6474 (tp30) REVERT: B 347 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6931 (mt) REVERT: B 393 GLU cc_start: 0.5942 (mp0) cc_final: 0.5281 (tt0) REVERT: B 409 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.5646 (t80) REVERT: B 443 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5217 (mtmt) REVERT: C 7 LYS cc_start: 0.6495 (mtpp) cc_final: 0.5961 (mtpm) REVERT: C 20 MET cc_start: 0.3475 (OUTLIER) cc_final: 0.1891 (tpp) REVERT: C 80 HIS cc_start: 0.5282 (t-90) cc_final: 0.5006 (t-90) REVERT: C 210 MET cc_start: 0.5905 (ppp) cc_final: 0.5120 (tpt) REVERT: C 233 LYS cc_start: 0.3994 (mttt) cc_final: 0.3142 (mmtt) REVERT: C 271 ARG cc_start: 0.6629 (mtt-85) cc_final: 0.6319 (ptp-110) REVERT: C 287 GLU cc_start: 0.7286 (mp0) cc_final: 0.6960 (mm-30) REVERT: C 288 ASP cc_start: 0.6397 (OUTLIER) cc_final: 0.6162 (m-30) REVERT: C 289 ILE cc_start: 0.6052 (pt) cc_final: 0.5004 (mm) REVERT: C 302 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5665 (mt-10) REVERT: C 304 GLU cc_start: 0.7226 (tt0) cc_final: 0.6930 (tt0) REVERT: C 311 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6701 (tt) REVERT: C 315 ARG cc_start: 0.6855 (tpp-160) cc_final: 0.6330 (tpp80) REVERT: C 336 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6265 (pp20) REVERT: C 343 LEU cc_start: 0.8358 (mt) cc_final: 0.8004 (mp) REVERT: C 371 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6312 (pp20) REVERT: C 482 ILE cc_start: 0.6524 (pt) cc_final: 0.6006 (pt) REVERT: C 731 MET cc_start: 0.3882 (ptt) cc_final: 0.3435 (ptp) outliers start: 141 outliers final: 72 residues processed: 760 average time/residue: 1.4939 time to fit residues: 1401.9753 Evaluate side-chains 748 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 653 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1057 LYS Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1485 SER Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2417 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3242 MET Chi-restraints excluded: chain A residue 3262 LEU Chi-restraints excluded: chain A residue 3270 ASP Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 481 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 454 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 344 optimal weight: 0.0020 chunk 266 optimal weight: 0.5980 chunk 396 optimal weight: 0.6980 chunk 263 optimal weight: 1.9990 chunk 469 optimal weight: 0.6980 chunk 293 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 415 GLN A 533 HIS A 720 GLN A1385 ASN A1738 ASN A1754 GLN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN A3516 HIS A3524 ASN A3762 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40414 Z= 0.226 Angle : 0.674 12.238 54841 Z= 0.336 Chirality : 0.042 0.277 6243 Planarity : 0.005 0.057 6791 Dihedral : 12.132 170.755 5773 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.58 % Favored : 90.40 % Rotamer: Outliers : 3.54 % Allowed : 19.68 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 4795 helix: 0.62 (0.10), residues: 2837 sheet: -0.66 (0.36), residues: 210 loop : -2.67 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3498 HIS 0.011 0.001 HIS A1367 PHE 0.028 0.002 PHE A2260 TYR 0.024 0.002 TYR A3442 ARG 0.014 0.001 ARG A2228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 671 time to evaluate : 4.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7045 (mm) REVERT: A 61 ARG cc_start: 0.6891 (mmt180) cc_final: 0.6583 (mpt90) REVERT: A 80 GLU cc_start: 0.6300 (mp0) cc_final: 0.5945 (mp0) REVERT: A 143 LEU cc_start: 0.6968 (mt) cc_final: 0.6571 (mt) REVERT: A 146 GLU cc_start: 0.6145 (tp30) cc_final: 0.5936 (mm-30) REVERT: A 172 GLU cc_start: 0.7837 (tt0) cc_final: 0.6743 (tm-30) REVERT: A 191 ASN cc_start: 0.7716 (m-40) cc_final: 0.7381 (m110) REVERT: A 243 GLN cc_start: 0.6421 (tp40) cc_final: 0.5632 (mp10) REVERT: A 263 LYS cc_start: 0.7174 (mptt) cc_final: 0.6543 (mppt) REVERT: A 272 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6380 (pp) REVERT: A 326 MET cc_start: 0.6134 (mtp) cc_final: 0.5566 (mtm) REVERT: A 329 LYS cc_start: 0.6829 (mtmp) cc_final: 0.6520 (mtmm) REVERT: A 340 TYR cc_start: 0.6806 (t80) cc_final: 0.6370 (t80) REVERT: A 342 MET cc_start: 0.6230 (mmt) cc_final: 0.5914 (mmm) REVERT: A 373 CYS cc_start: 0.6847 (m) cc_final: 0.6407 (m) REVERT: A 379 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.5928 (mtpm) REVERT: A 380 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.4920 (m-30) REVERT: A 395 MET cc_start: 0.6201 (ptm) cc_final: 0.5674 (ptm) REVERT: A 423 TYR cc_start: 0.7321 (m-80) cc_final: 0.6558 (m-80) REVERT: A 441 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.6277 (ttt) REVERT: A 442 GLN cc_start: 0.6148 (tp-100) cc_final: 0.5840 (tp-100) REVERT: A 453 MET cc_start: 0.6615 (tpp) cc_final: 0.6023 (tpp) REVERT: A 524 TYR cc_start: 0.6800 (p90) cc_final: 0.6571 (p90) REVERT: A 578 LYS cc_start: 0.6922 (ptpt) cc_final: 0.6413 (ptpp) REVERT: A 631 ARG cc_start: 0.5092 (ttm110) cc_final: 0.4776 (mtp-110) REVERT: A 659 ARG cc_start: 0.7007 (ptt90) cc_final: 0.5923 (mtm110) REVERT: A 669 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6831 (mp) REVERT: A 746 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6761 (ttp-110) REVERT: A 767 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: A 775 GLU cc_start: 0.6715 (tt0) cc_final: 0.5956 (mt-10) REVERT: A 781 ASP cc_start: 0.6669 (m-30) cc_final: 0.6170 (m-30) REVERT: A 783 HIS cc_start: 0.6481 (m-70) cc_final: 0.6202 (m-70) REVERT: A 784 VAL cc_start: 0.5762 (m) cc_final: 0.5452 (p) REVERT: A 786 GLN cc_start: 0.7491 (tm-30) cc_final: 0.6641 (tm130) REVERT: A 823 GLN cc_start: 0.5773 (tt0) cc_final: 0.5180 (mm-40) REVERT: A 828 LYS cc_start: 0.6756 (mmmm) cc_final: 0.6326 (mttp) REVERT: A 851 ILE cc_start: 0.7207 (mm) cc_final: 0.6968 (mm) REVERT: A 857 GLN cc_start: 0.7016 (mt0) cc_final: 0.6117 (mm110) REVERT: A 879 MET cc_start: 0.7401 (ttm) cc_final: 0.7177 (ttm) REVERT: A 881 LYS cc_start: 0.6525 (mttp) cc_final: 0.5822 (mmmt) REVERT: A 889 GLU cc_start: 0.6364 (tm-30) cc_final: 0.5741 (tp30) REVERT: A 900 GLU cc_start: 0.4564 (tm-30) cc_final: 0.4331 (tm-30) REVERT: A 937 MET cc_start: 0.7503 (mtt) cc_final: 0.7280 (mtt) REVERT: A 944 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5855 (mttp) REVERT: A 983 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6430 (mt) REVERT: A 989 MET cc_start: 0.5991 (mmt) cc_final: 0.5639 (mmm) REVERT: A 990 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.6052 (pm20) REVERT: A 1014 LEU cc_start: 0.5005 (mt) cc_final: 0.4770 (mt) REVERT: A 1015 ASP cc_start: 0.6139 (m-30) cc_final: 0.5791 (m-30) REVERT: A 1061 LYS cc_start: 0.6902 (mtpm) cc_final: 0.6532 (mtpp) REVERT: A 1076 LEU cc_start: 0.6027 (tp) cc_final: 0.5689 (tm) REVERT: A 1083 ASN cc_start: 0.6160 (t0) cc_final: 0.5673 (m-40) REVERT: A 1123 THR cc_start: 0.6107 (t) cc_final: 0.5626 (t) REVERT: A 1125 GLN cc_start: 0.6820 (tp40) cc_final: 0.6524 (tp-100) REVERT: A 1332 TYR cc_start: 0.4877 (t80) cc_final: 0.4490 (t80) REVERT: A 1392 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6939 (mmm) REVERT: A 1509 GLN cc_start: 0.5821 (tt0) cc_final: 0.4922 (tp-100) REVERT: A 1531 LEU cc_start: 0.7149 (pp) cc_final: 0.6746 (tp) REVERT: A 1576 ASP cc_start: 0.5307 (p0) cc_final: 0.4985 (m-30) REVERT: A 1607 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6062 (mm-30) REVERT: A 1627 LYS cc_start: 0.7206 (mmpt) cc_final: 0.6763 (mtmt) REVERT: A 1735 ARG cc_start: 0.5517 (mtm-85) cc_final: 0.5257 (ptp-170) REVERT: A 1761 LEU cc_start: 0.6043 (mt) cc_final: 0.5794 (mp) REVERT: A 1762 MET cc_start: 0.4696 (mmp) cc_final: 0.4387 (mmp) REVERT: A 1775 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5536 (mt-10) REVERT: A 1795 VAL cc_start: 0.6409 (t) cc_final: 0.5986 (t) REVERT: A 1799 GLU cc_start: 0.5804 (mt-10) cc_final: 0.5243 (mt-10) REVERT: A 1849 ASP cc_start: 0.6028 (t0) cc_final: 0.4886 (m-30) REVERT: A 1971 PRO cc_start: 0.4009 (Cg_endo) cc_final: 0.3792 (Cg_exo) REVERT: A 2042 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5204 (tm-30) REVERT: A 2085 MET cc_start: 0.6276 (pmm) cc_final: 0.5866 (pmm) REVERT: A 2091 HIS cc_start: 0.6199 (t-90) cc_final: 0.5955 (t70) REVERT: A 2126 MET cc_start: 0.5735 (mtt) cc_final: 0.5431 (mtt) REVERT: A 2127 LYS cc_start: 0.6453 (mptt) cc_final: 0.5992 (mptt) REVERT: A 2162 LYS cc_start: 0.7599 (mttp) cc_final: 0.7359 (mmmt) REVERT: A 2163 HIS cc_start: 0.6869 (m90) cc_final: 0.6151 (m-70) REVERT: A 2170 GLN cc_start: 0.6153 (tt0) cc_final: 0.5874 (tt0) REVERT: A 2221 LYS cc_start: 0.5993 (tttm) cc_final: 0.5671 (ttmm) REVERT: A 2227 LYS cc_start: 0.5887 (tptt) cc_final: 0.5605 (tppp) REVERT: A 2239 LYS cc_start: 0.6350 (tmmt) cc_final: 0.5840 (ttpt) REVERT: A 2243 GLU cc_start: 0.6629 (tm-30) cc_final: 0.6088 (pt0) REVERT: A 2292 CYS cc_start: 0.6584 (OUTLIER) cc_final: 0.5745 (p) REVERT: A 2356 MET cc_start: 0.6100 (mtm) cc_final: 0.5791 (mtp) REVERT: A 2357 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6276 (mp0) REVERT: A 2362 VAL cc_start: 0.7649 (t) cc_final: 0.7290 (m) REVERT: A 2369 LYS cc_start: 0.7788 (mttt) cc_final: 0.6508 (mmpt) REVERT: A 2427 ARG cc_start: 0.6855 (tpt90) cc_final: 0.6299 (tpm-80) REVERT: A 2430 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5670 (tt0) REVERT: A 2434 VAL cc_start: 0.6978 (t) cc_final: 0.6674 (p) REVERT: A 2447 LYS cc_start: 0.7823 (mmpt) cc_final: 0.7378 (mmpt) REVERT: A 2498 ILE cc_start: 0.7100 (pt) cc_final: 0.6803 (pp) REVERT: A 2504 ASP cc_start: 0.5995 (m-30) cc_final: 0.5349 (m-30) REVERT: A 2522 ARG cc_start: 0.5536 (tmt170) cc_final: 0.5243 (ttm-80) REVERT: A 2551 GLU cc_start: 0.8047 (tt0) cc_final: 0.7618 (tt0) REVERT: A 2795 GLN cc_start: 0.6518 (tm-30) cc_final: 0.6176 (tp40) REVERT: A 2818 LYS cc_start: 0.7424 (tttt) cc_final: 0.6692 (tttm) REVERT: A 2839 ASP cc_start: 0.5736 (m-30) cc_final: 0.5336 (m-30) REVERT: A 2864 GLN cc_start: 0.7086 (mm-40) cc_final: 0.5938 (tm-30) REVERT: A 2935 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6549 (mm-30) REVERT: A 2958 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6402 (pp) REVERT: A 3007 GLU cc_start: 0.7197 (mp0) cc_final: 0.6281 (mm-30) REVERT: A 3067 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6081 (tttp) REVERT: A 3090 TYR cc_start: 0.7520 (m-80) cc_final: 0.6470 (m-80) REVERT: A 3140 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6694 (mt-10) REVERT: A 3158 LYS cc_start: 0.6649 (mtpp) cc_final: 0.6366 (mtpt) REVERT: A 3172 LYS cc_start: 0.7641 (ttmm) cc_final: 0.7333 (ttmt) REVERT: A 3173 MET cc_start: 0.7046 (mmm) cc_final: 0.6773 (mpp) REVERT: A 3191 SER cc_start: 0.7551 (t) cc_final: 0.7252 (m) REVERT: A 3237 SER cc_start: 0.7539 (t) cc_final: 0.7333 (m) REVERT: A 3284 SER cc_start: 0.7691 (p) cc_final: 0.7399 (p) REVERT: A 3287 ARG cc_start: 0.6621 (ptm160) cc_final: 0.6155 (ptm-80) REVERT: A 3289 ARG cc_start: 0.6647 (mpt90) cc_final: 0.6025 (mpt-90) REVERT: A 3327 ASN cc_start: 0.5800 (m-40) cc_final: 0.5245 (m110) REVERT: A 3387 GLU cc_start: 0.6216 (tp30) cc_final: 0.5700 (tt0) REVERT: A 3520 GLU cc_start: 0.4639 (pt0) cc_final: 0.4209 (tp30) REVERT: A 3718 ARG cc_start: 0.5495 (mpp80) cc_final: 0.5134 (mpp80) REVERT: A 3734 ARG cc_start: 0.6269 (tpp80) cc_final: 0.5392 (tpp-160) REVERT: A 3747 GLU cc_start: 0.7044 (tt0) cc_final: 0.6784 (tt0) REVERT: A 3772 ASN cc_start: 0.6933 (p0) cc_final: 0.6314 (p0) REVERT: A 3796 MET cc_start: 0.8093 (mmp) cc_final: 0.7400 (mmm) REVERT: A 3863 ASN cc_start: 0.6302 (p0) cc_final: 0.6064 (p0) REVERT: A 3869 THR cc_start: 0.6319 (m) cc_final: 0.6062 (m) REVERT: A 3877 LYS cc_start: 0.7167 (mtmm) cc_final: 0.6739 (tptp) REVERT: A 3932 MET cc_start: 0.7604 (mmm) cc_final: 0.7166 (mmm) REVERT: A 4089 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.5944 (pt) REVERT: A 4098 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6558 (mp) REVERT: A 4108 MET cc_start: 0.7603 (ttm) cc_final: 0.7313 (mtt) REVERT: B 78 SER cc_start: 0.7933 (m) cc_final: 0.7714 (m) REVERT: B 130 ARG cc_start: 0.5737 (mtp180) cc_final: 0.5474 (mtp85) REVERT: B 160 LYS cc_start: 0.7453 (tppp) cc_final: 0.6876 (tmtt) REVERT: B 165 ARG cc_start: 0.6864 (ttp-110) cc_final: 0.6101 (mtp85) REVERT: B 192 ASP cc_start: 0.5461 (t70) cc_final: 0.5083 (t70) REVERT: B 281 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7148 (pp) REVERT: B 294 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6206 (mt-10) REVERT: B 317 LYS cc_start: 0.5838 (mttt) cc_final: 0.5340 (mmmt) REVERT: B 333 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6673 (mt-10) REVERT: B 335 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6411 (tp30) REVERT: B 393 GLU cc_start: 0.5849 (mp0) cc_final: 0.5217 (tt0) REVERT: B 409 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.5617 (t80) REVERT: B 443 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5199 (mtmt) REVERT: C 7 LYS cc_start: 0.6533 (mtpp) cc_final: 0.6037 (mtpm) REVERT: C 20 MET cc_start: 0.3450 (OUTLIER) cc_final: 0.1885 (tpp) REVERT: C 80 HIS cc_start: 0.5217 (t-90) cc_final: 0.4944 (t-90) REVERT: C 210 MET cc_start: 0.5838 (ppp) cc_final: 0.5080 (tpt) REVERT: C 233 LYS cc_start: 0.3987 (mttt) cc_final: 0.3144 (mmtt) REVERT: C 259 ILE cc_start: 0.5547 (OUTLIER) cc_final: 0.5256 (tt) REVERT: C 271 ARG cc_start: 0.6636 (mtt-85) cc_final: 0.6309 (ptp-110) REVERT: C 286 LYS cc_start: 0.6672 (ttpt) cc_final: 0.6221 (ttpp) REVERT: C 287 GLU cc_start: 0.7307 (mp0) cc_final: 0.6776 (mp0) REVERT: C 288 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6163 (m-30) REVERT: C 289 ILE cc_start: 0.6043 (pt) cc_final: 0.4981 (mm) REVERT: C 302 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5854 (mt-10) REVERT: C 304 GLU cc_start: 0.7314 (tt0) cc_final: 0.6995 (tt0) REVERT: C 311 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6707 (tt) REVERT: C 315 ARG cc_start: 0.6788 (tpp-160) cc_final: 0.6249 (tpp80) REVERT: C 336 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6250 (pp20) REVERT: C 343 LEU cc_start: 0.8418 (mt) cc_final: 0.8068 (mp) REVERT: C 356 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: C 371 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6213 (pp20) REVERT: C 388 ASP cc_start: 0.5511 (t0) cc_final: 0.5212 (m-30) REVERT: C 427 MET cc_start: 0.7361 (ppp) cc_final: 0.6806 (pp-130) REVERT: C 482 ILE cc_start: 0.6701 (pt) cc_final: 0.6059 (pt) REVERT: C 552 GLU cc_start: 0.7101 (pt0) cc_final: 0.6376 (pp20) outliers start: 147 outliers final: 85 residues processed: 751 average time/residue: 1.5103 time to fit residues: 1400.0238 Evaluate side-chains 774 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 660 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1057 LYS Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1485 SER Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2292 CYS Chi-restraints excluded: chain A residue 2780 LEU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2820 MET Chi-restraints excluded: chain A residue 2958 LEU Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3242 MET Chi-restraints excluded: chain A residue 3262 LEU Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 290 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 280 optimal weight: 0.0980 chunk 141 optimal weight: 0.9980 chunk 92 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 chunk 319 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 368 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 250 ASN A 415 GLN A 533 HIS A 720 GLN A1385 ASN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2275 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN A3383 GLN A3516 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS C 411 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 40414 Z= 0.224 Angle : 0.675 12.033 54841 Z= 0.336 Chirality : 0.042 0.307 6243 Planarity : 0.005 0.064 6791 Dihedral : 12.136 173.440 5773 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.26 % Allowed : 20.63 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 4795 helix: 0.64 (0.10), residues: 2838 sheet: -0.62 (0.36), residues: 210 loop : -2.67 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A3498 HIS 0.014 0.001 HIS C 246 PHE 0.028 0.002 PHE A2260 TYR 0.030 0.002 TYR A3442 ARG 0.014 0.001 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 666 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7051 (mm) REVERT: A 41 GLU cc_start: 0.5811 (tt0) cc_final: 0.4931 (tp30) REVERT: A 61 ARG cc_start: 0.6892 (mmt180) cc_final: 0.6580 (mpt90) REVERT: A 80 GLU cc_start: 0.6303 (mp0) cc_final: 0.5948 (mp0) REVERT: A 143 LEU cc_start: 0.6910 (mt) cc_final: 0.6489 (mt) REVERT: A 146 GLU cc_start: 0.6140 (tp30) cc_final: 0.5935 (mm-30) REVERT: A 172 GLU cc_start: 0.7839 (tt0) cc_final: 0.6727 (tm-30) REVERT: A 191 ASN cc_start: 0.7721 (m-40) cc_final: 0.7378 (m110) REVERT: A 243 GLN cc_start: 0.6424 (tp40) cc_final: 0.5631 (mp10) REVERT: A 263 LYS cc_start: 0.7166 (mptt) cc_final: 0.6531 (mppt) REVERT: A 272 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6308 (pp) REVERT: A 326 MET cc_start: 0.6041 (mtp) cc_final: 0.5491 (mtm) REVERT: A 329 LYS cc_start: 0.6831 (mtmp) cc_final: 0.6529 (mtmm) REVERT: A 332 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6106 (tp30) REVERT: A 338 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6719 (tt) REVERT: A 340 TYR cc_start: 0.6811 (t80) cc_final: 0.6365 (t80) REVERT: A 342 MET cc_start: 0.6237 (mmt) cc_final: 0.6031 (mmm) REVERT: A 343 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5880 (mm-30) REVERT: A 373 CYS cc_start: 0.6990 (m) cc_final: 0.6579 (m) REVERT: A 379 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5959 (mtpm) REVERT: A 380 ASP cc_start: 0.6061 (OUTLIER) cc_final: 0.5100 (m-30) REVERT: A 395 MET cc_start: 0.6177 (ptm) cc_final: 0.5634 (ptm) REVERT: A 423 TYR cc_start: 0.7325 (m-80) cc_final: 0.6558 (m-80) REVERT: A 441 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6323 (ttt) REVERT: A 442 GLN cc_start: 0.6165 (tp-100) cc_final: 0.5868 (tp-100) REVERT: A 453 MET cc_start: 0.6622 (tpp) cc_final: 0.6128 (tpp) REVERT: A 524 TYR cc_start: 0.6791 (p90) cc_final: 0.6583 (p90) REVERT: A 578 LYS cc_start: 0.6887 (ptpt) cc_final: 0.6382 (ptpp) REVERT: A 631 ARG cc_start: 0.5038 (ttm110) cc_final: 0.4765 (mtp-110) REVERT: A 659 ARG cc_start: 0.7031 (ptt90) cc_final: 0.5949 (mtm110) REVERT: A 669 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6770 (mp) REVERT: A 746 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6781 (ttp-110) REVERT: A 767 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6669 (tt0) REVERT: A 775 GLU cc_start: 0.6672 (tt0) cc_final: 0.5967 (mp0) REVERT: A 781 ASP cc_start: 0.6666 (m-30) cc_final: 0.6169 (m-30) REVERT: A 783 HIS cc_start: 0.6501 (m-70) cc_final: 0.6229 (m-70) REVERT: A 784 VAL cc_start: 0.5753 (m) cc_final: 0.5444 (p) REVERT: A 786 GLN cc_start: 0.7483 (tm-30) cc_final: 0.6638 (tm130) REVERT: A 823 GLN cc_start: 0.5770 (tt0) cc_final: 0.5479 (tt0) REVERT: A 828 LYS cc_start: 0.6763 (mmmm) cc_final: 0.6333 (mttp) REVERT: A 857 GLN cc_start: 0.6945 (mt0) cc_final: 0.6089 (mm110) REVERT: A 879 MET cc_start: 0.7390 (ttm) cc_final: 0.7158 (ttm) REVERT: A 881 LYS cc_start: 0.6539 (mttp) cc_final: 0.5825 (mmmt) REVERT: A 889 GLU cc_start: 0.6378 (tm-30) cc_final: 0.5747 (tp30) REVERT: A 900 GLU cc_start: 0.4667 (tm-30) cc_final: 0.4362 (tm-30) REVERT: A 937 MET cc_start: 0.7391 (mtt) cc_final: 0.7161 (mtt) REVERT: A 944 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5871 (mttp) REVERT: A 983 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6438 (mt) REVERT: A 989 MET cc_start: 0.5929 (mmt) cc_final: 0.5607 (mmm) REVERT: A 990 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6051 (pm20) REVERT: A 1014 LEU cc_start: 0.4998 (mt) cc_final: 0.4760 (mt) REVERT: A 1015 ASP cc_start: 0.6121 (m-30) cc_final: 0.5772 (m-30) REVERT: A 1061 LYS cc_start: 0.6898 (mtpm) cc_final: 0.6530 (mtpp) REVERT: A 1076 LEU cc_start: 0.6022 (tp) cc_final: 0.5761 (tm) REVERT: A 1083 ASN cc_start: 0.6159 (t0) cc_final: 0.5675 (m-40) REVERT: A 1125 GLN cc_start: 0.6819 (tp40) cc_final: 0.6531 (tp-100) REVERT: A 1332 TYR cc_start: 0.4666 (t80) cc_final: 0.4267 (t80) REVERT: A 1509 GLN cc_start: 0.5829 (tt0) cc_final: 0.4929 (tp-100) REVERT: A 1531 LEU cc_start: 0.7116 (pp) cc_final: 0.6752 (tp) REVERT: A 1576 ASP cc_start: 0.5701 (p0) cc_final: 0.5385 (m-30) REVERT: A 1607 GLU cc_start: 0.6433 (mm-30) cc_final: 0.6072 (mm-30) REVERT: A 1627 LYS cc_start: 0.7187 (mmpt) cc_final: 0.6725 (mtmt) REVERT: A 1735 ARG cc_start: 0.5515 (mtm-85) cc_final: 0.5255 (ptp-170) REVERT: A 1761 LEU cc_start: 0.5953 (mt) cc_final: 0.5731 (mp) REVERT: A 1762 MET cc_start: 0.4684 (mmp) cc_final: 0.4390 (mmp) REVERT: A 1775 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5535 (mt-10) REVERT: A 1784 ARG cc_start: 0.5099 (ttp-110) cc_final: 0.4154 (mtm110) REVERT: A 1795 VAL cc_start: 0.6721 (t) cc_final: 0.6268 (t) REVERT: A 1799 GLU cc_start: 0.5806 (mt-10) cc_final: 0.5241 (mt-10) REVERT: A 1849 ASP cc_start: 0.5982 (t0) cc_final: 0.4883 (m-30) REVERT: A 1852 LYS cc_start: 0.5486 (mttm) cc_final: 0.5168 (mttp) REVERT: A 1971 PRO cc_start: 0.4013 (Cg_endo) cc_final: 0.3787 (Cg_exo) REVERT: A 2042 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5207 (tm-30) REVERT: A 2085 MET cc_start: 0.6313 (pmm) cc_final: 0.5937 (pmm) REVERT: A 2091 HIS cc_start: 0.6200 (t-90) cc_final: 0.5804 (t70) REVERT: A 2126 MET cc_start: 0.5726 (mtt) cc_final: 0.5440 (mtt) REVERT: A 2127 LYS cc_start: 0.6455 (mptt) cc_final: 0.5988 (mptt) REVERT: A 2162 LYS cc_start: 0.7594 (mttp) cc_final: 0.7361 (mmmt) REVERT: A 2163 HIS cc_start: 0.6866 (m90) cc_final: 0.6121 (m-70) REVERT: A 2170 GLN cc_start: 0.6235 (tt0) cc_final: 0.5960 (tt0) REVERT: A 2221 LYS cc_start: 0.6009 (tttm) cc_final: 0.5688 (ttmm) REVERT: A 2227 LYS cc_start: 0.5897 (tptt) cc_final: 0.5623 (tppp) REVERT: A 2239 LYS cc_start: 0.6360 (tmmt) cc_final: 0.5837 (ttpt) REVERT: A 2243 GLU cc_start: 0.6624 (tm-30) cc_final: 0.6085 (pt0) REVERT: A 2292 CYS cc_start: 0.6584 (OUTLIER) cc_final: 0.5750 (p) REVERT: A 2356 MET cc_start: 0.6328 (mtm) cc_final: 0.6011 (mtp) REVERT: A 2357 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6280 (mp0) REVERT: A 2362 VAL cc_start: 0.7652 (t) cc_final: 0.7284 (m) REVERT: A 2369 LYS cc_start: 0.7786 (mttt) cc_final: 0.6505 (mmpt) REVERT: A 2427 ARG cc_start: 0.6846 (tpt90) cc_final: 0.6270 (tpm-80) REVERT: A 2430 GLU cc_start: 0.6103 (mm-30) cc_final: 0.5742 (tt0) REVERT: A 2434 VAL cc_start: 0.6984 (t) cc_final: 0.6683 (p) REVERT: A 2447 LYS cc_start: 0.7828 (mmpt) cc_final: 0.7405 (mmpt) REVERT: A 2450 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7215 (tt0) REVERT: A 2498 ILE cc_start: 0.7098 (pt) cc_final: 0.6803 (pp) REVERT: A 2504 ASP cc_start: 0.5931 (m-30) cc_final: 0.5318 (m-30) REVERT: A 2522 ARG cc_start: 0.5527 (tmt170) cc_final: 0.5244 (ttm-80) REVERT: A 2551 GLU cc_start: 0.8053 (tt0) cc_final: 0.7618 (tt0) REVERT: A 2795 GLN cc_start: 0.6510 (tm-30) cc_final: 0.6170 (tp40) REVERT: A 2818 LYS cc_start: 0.7409 (tttt) cc_final: 0.6693 (tttm) REVERT: A 2864 GLN cc_start: 0.7082 (mm-40) cc_final: 0.5936 (tm-30) REVERT: A 2935 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6547 (mm-30) REVERT: A 2958 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6398 (pp) REVERT: A 3007 GLU cc_start: 0.7192 (mp0) cc_final: 0.6281 (mm-30) REVERT: A 3067 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6098 (tttp) REVERT: A 3090 TYR cc_start: 0.7515 (m-80) cc_final: 0.6463 (m-80) REVERT: A 3140 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6499 (mt-10) REVERT: A 3158 LYS cc_start: 0.6680 (mtpp) cc_final: 0.6400 (mtpt) REVERT: A 3159 ARG cc_start: 0.5559 (ttp-110) cc_final: 0.5241 (ttp-110) REVERT: A 3172 LYS cc_start: 0.7587 (ttmm) cc_final: 0.7105 (ttmt) REVERT: A 3173 MET cc_start: 0.7005 (mmm) cc_final: 0.6602 (mpp) REVERT: A 3237 SER cc_start: 0.7537 (t) cc_final: 0.7330 (m) REVERT: A 3287 ARG cc_start: 0.6585 (ptm160) cc_final: 0.6107 (ptm-80) REVERT: A 3289 ARG cc_start: 0.6846 (mpt90) cc_final: 0.6232 (mpt-90) REVERT: A 3327 ASN cc_start: 0.5670 (m-40) cc_final: 0.5086 (m110) REVERT: A 3387 GLU cc_start: 0.6226 (tp30) cc_final: 0.5709 (tt0) REVERT: A 3520 GLU cc_start: 0.4882 (pt0) cc_final: 0.4336 (tp30) REVERT: A 3718 ARG cc_start: 0.5494 (mpp80) cc_final: 0.5124 (mpp80) REVERT: A 3734 ARG cc_start: 0.6110 (tpp80) cc_final: 0.5226 (tpp-160) REVERT: A 3772 ASN cc_start: 0.6948 (p0) cc_final: 0.6345 (p0) REVERT: A 3796 MET cc_start: 0.8083 (mmp) cc_final: 0.7603 (mmm) REVERT: A 3824 GLU cc_start: 0.6160 (pt0) cc_final: 0.4907 (pm20) REVERT: A 3863 ASN cc_start: 0.6310 (p0) cc_final: 0.6075 (p0) REVERT: A 3869 THR cc_start: 0.6318 (m) cc_final: 0.6063 (m) REVERT: A 3877 LYS cc_start: 0.7176 (mtmm) cc_final: 0.6735 (tptp) REVERT: A 3932 MET cc_start: 0.7637 (mmm) cc_final: 0.7202 (mmm) REVERT: A 4089 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.5949 (pt) REVERT: A 4098 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6550 (mp) REVERT: A 4108 MET cc_start: 0.7603 (ttm) cc_final: 0.7312 (mtt) REVERT: B 78 SER cc_start: 0.7937 (m) cc_final: 0.7717 (m) REVERT: B 130 ARG cc_start: 0.5797 (mtp180) cc_final: 0.5501 (mtp85) REVERT: B 160 LYS cc_start: 0.7443 (tppp) cc_final: 0.6845 (tmtt) REVERT: B 165 ARG cc_start: 0.6847 (ttp-110) cc_final: 0.6095 (mtp85) REVERT: B 187 ARG cc_start: 0.7230 (mtm180) cc_final: 0.6773 (mtm110) REVERT: B 192 ASP cc_start: 0.5430 (t70) cc_final: 0.5058 (t70) REVERT: B 281 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7124 (pp) REVERT: B 294 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6190 (mt-10) REVERT: B 317 LYS cc_start: 0.5994 (mttt) cc_final: 0.5338 (mmmt) REVERT: B 333 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6698 (mt-10) REVERT: B 335 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6499 (tp30) REVERT: B 393 GLU cc_start: 0.5992 (mp0) cc_final: 0.5286 (tt0) REVERT: B 409 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.5625 (t80) REVERT: B 443 LYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5198 (mtmt) REVERT: C 7 LYS cc_start: 0.6472 (mtpp) cc_final: 0.5994 (mtpm) REVERT: C 20 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.1931 (tpp) REVERT: C 80 HIS cc_start: 0.5225 (t-90) cc_final: 0.4930 (t-90) REVERT: C 210 MET cc_start: 0.5893 (ppp) cc_final: 0.5096 (tpt) REVERT: C 233 LYS cc_start: 0.4009 (mttt) cc_final: 0.3182 (mmtt) REVERT: C 259 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.5201 (tt) REVERT: C 271 ARG cc_start: 0.6708 (mtt-85) cc_final: 0.6501 (mtt90) REVERT: C 286 LYS cc_start: 0.6681 (ttpt) cc_final: 0.6227 (ttpp) REVERT: C 287 GLU cc_start: 0.7315 (mp0) cc_final: 0.6781 (mp0) REVERT: C 288 ASP cc_start: 0.6443 (OUTLIER) cc_final: 0.6176 (m-30) REVERT: C 289 ILE cc_start: 0.6032 (pt) cc_final: 0.4980 (OUTLIER) REVERT: C 311 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6724 (tt) REVERT: C 336 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6210 (pp20) REVERT: C 343 LEU cc_start: 0.8346 (mt) cc_final: 0.7992 (mp) REVERT: C 356 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: C 371 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6221 (pp20) REVERT: C 388 ASP cc_start: 0.5061 (t0) cc_final: 0.4642 (m-30) REVERT: C 427 MET cc_start: 0.7488 (ppp) cc_final: 0.6874 (pp-130) REVERT: C 482 ILE cc_start: 0.6561 (pt) cc_final: 0.6000 (pt) REVERT: C 552 GLU cc_start: 0.7152 (pt0) cc_final: 0.6392 (pp20) REVERT: C 731 MET cc_start: 0.3767 (ptt) cc_final: 0.3361 (ptp) outliers start: 135 outliers final: 89 residues processed: 737 average time/residue: 1.4847 time to fit residues: 1348.7819 Evaluate side-chains 769 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 652 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1057 LYS Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2292 CYS Chi-restraints excluded: chain A residue 2566 THR Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2820 MET Chi-restraints excluded: chain A residue 2958 LEU Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3044 MET Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3242 MET Chi-restraints excluded: chain A residue 3262 LEU Chi-restraints excluded: chain A residue 3326 GLN Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 426 optimal weight: 9.9990 chunk 449 optimal weight: 2.9990 chunk 410 optimal weight: 0.5980 chunk 437 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 343 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 chunk 413 optimal weight: 0.0970 chunk 435 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 415 GLN A 533 HIS A 720 GLN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3166 ASN A3326 GLN A3516 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS C 411 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 40414 Z= 0.338 Angle : 0.747 12.098 54841 Z= 0.371 Chirality : 0.045 0.272 6243 Planarity : 0.005 0.060 6791 Dihedral : 12.241 173.487 5770 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.10 % Favored : 89.85 % Rotamer: Outliers : 3.30 % Allowed : 21.03 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 4795 helix: 0.41 (0.10), residues: 2856 sheet: -0.69 (0.36), residues: 210 loop : -2.67 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A3498 HIS 0.030 0.001 HIS C 246 PHE 0.039 0.002 PHE A2260 TYR 0.037 0.002 TYR A3442 ARG 0.013 0.001 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 664 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7053 (mm) REVERT: A 41 GLU cc_start: 0.5819 (tt0) cc_final: 0.4936 (tp30) REVERT: A 80 GLU cc_start: 0.6240 (mp0) cc_final: 0.5862 (mp0) REVERT: A 143 LEU cc_start: 0.7034 (mt) cc_final: 0.6591 (mt) REVERT: A 146 GLU cc_start: 0.6252 (tp30) cc_final: 0.6016 (mm-30) REVERT: A 172 GLU cc_start: 0.7777 (tt0) cc_final: 0.6544 (tm-30) REVERT: A 191 ASN cc_start: 0.7690 (m-40) cc_final: 0.7314 (m110) REVERT: A 243 GLN cc_start: 0.6469 (tp40) cc_final: 0.5661 (mp10) REVERT: A 263 LYS cc_start: 0.7207 (mptt) cc_final: 0.6558 (mppt) REVERT: A 326 MET cc_start: 0.6031 (mtp) cc_final: 0.5453 (mtm) REVERT: A 329 LYS cc_start: 0.6846 (mtmp) cc_final: 0.6557 (mtmm) REVERT: A 338 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6721 (tt) REVERT: A 340 TYR cc_start: 0.6841 (t80) cc_final: 0.6333 (t80) REVERT: A 342 MET cc_start: 0.6205 (mmt) cc_final: 0.5842 (mmm) REVERT: A 343 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5837 (mm-30) REVERT: A 373 CYS cc_start: 0.6868 (m) cc_final: 0.6425 (m) REVERT: A 379 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.6041 (mtpm) REVERT: A 380 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5213 (m-30) REVERT: A 395 MET cc_start: 0.6031 (ptm) cc_final: 0.5559 (ptm) REVERT: A 441 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6244 (ttt) REVERT: A 442 GLN cc_start: 0.6163 (tp-100) cc_final: 0.5872 (tp-100) REVERT: A 476 ARG cc_start: 0.6682 (mtp-110) cc_final: 0.6114 (mmm160) REVERT: A 578 LYS cc_start: 0.6882 (ptpt) cc_final: 0.6390 (ptpp) REVERT: A 669 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 746 ARG cc_start: 0.7185 (ttp-170) cc_final: 0.6807 (ttp-110) REVERT: A 767 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: A 775 GLU cc_start: 0.6686 (tt0) cc_final: 0.5955 (mp0) REVERT: A 781 ASP cc_start: 0.6667 (m-30) cc_final: 0.6188 (m-30) REVERT: A 783 HIS cc_start: 0.6460 (m-70) cc_final: 0.6187 (m-70) REVERT: A 784 VAL cc_start: 0.5815 (m) cc_final: 0.5438 (p) REVERT: A 786 GLN cc_start: 0.7558 (tm-30) cc_final: 0.6849 (tm-30) REVERT: A 823 GLN cc_start: 0.5809 (tt0) cc_final: 0.5573 (tt0) REVERT: A 828 LYS cc_start: 0.6800 (mmmm) cc_final: 0.6376 (mttp) REVERT: A 849 GLU cc_start: 0.5870 (pm20) cc_final: 0.5408 (pt0) REVERT: A 857 GLN cc_start: 0.6979 (mt0) cc_final: 0.6101 (mm110) REVERT: A 879 MET cc_start: 0.7408 (ttm) cc_final: 0.7176 (ttm) REVERT: A 881 LYS cc_start: 0.6589 (mttp) cc_final: 0.5870 (mmmt) REVERT: A 889 GLU cc_start: 0.6358 (tm-30) cc_final: 0.5760 (tp30) REVERT: A 944 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5881 (mttp) REVERT: A 983 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6294 (mt) REVERT: A 989 MET cc_start: 0.5981 (mmt) cc_final: 0.5510 (mmm) REVERT: A 990 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6077 (pm20) REVERT: A 1015 ASP cc_start: 0.6178 (m-30) cc_final: 0.5848 (m-30) REVERT: A 1061 LYS cc_start: 0.6968 (mtpm) cc_final: 0.6617 (mtpp) REVERT: A 1076 LEU cc_start: 0.6080 (tp) cc_final: 0.5813 (tm) REVERT: A 1083 ASN cc_start: 0.5969 (t0) cc_final: 0.5486 (m-40) REVERT: A 1125 GLN cc_start: 0.6812 (tp40) cc_final: 0.5951 (tp-100) REVERT: A 1129 ASP cc_start: 0.5260 (t70) cc_final: 0.4228 (m-30) REVERT: A 1136 ARG cc_start: 0.5196 (ptp90) cc_final: 0.4860 (mtm110) REVERT: A 1332 TYR cc_start: 0.4614 (t80) cc_final: 0.4184 (t80) REVERT: A 1509 GLN cc_start: 0.5882 (tt0) cc_final: 0.5144 (tp-100) REVERT: A 1531 LEU cc_start: 0.7102 (pp) cc_final: 0.6680 (tp) REVERT: A 1576 ASP cc_start: 0.5435 (p0) cc_final: 0.5025 (m-30) REVERT: A 1607 GLU cc_start: 0.6356 (mm-30) cc_final: 0.6039 (mm-30) REVERT: A 1627 LYS cc_start: 0.7192 (mmpt) cc_final: 0.6733 (mtmt) REVERT: A 1735 ARG cc_start: 0.5627 (mtm-85) cc_final: 0.5296 (ptm160) REVERT: A 1761 LEU cc_start: 0.5958 (mt) cc_final: 0.5724 (mp) REVERT: A 1762 MET cc_start: 0.4592 (mmp) cc_final: 0.4158 (mmp) REVERT: A 1775 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5637 (mt-10) REVERT: A 1784 ARG cc_start: 0.5296 (ttp-110) cc_final: 0.4361 (mtm110) REVERT: A 1799 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5361 (mt-10) REVERT: A 1849 ASP cc_start: 0.6030 (t0) cc_final: 0.4912 (m-30) REVERT: A 1971 PRO cc_start: 0.4023 (Cg_endo) cc_final: 0.3795 (Cg_exo) REVERT: A 2042 GLN cc_start: 0.6144 (OUTLIER) cc_final: 0.5104 (tm-30) REVERT: A 2085 MET cc_start: 0.6273 (pmm) cc_final: 0.5930 (pmm) REVERT: A 2126 MET cc_start: 0.5844 (mtt) cc_final: 0.5561 (mtt) REVERT: A 2127 LYS cc_start: 0.6290 (mptt) cc_final: 0.5780 (mptt) REVERT: A 2170 GLN cc_start: 0.6437 (tt0) cc_final: 0.6172 (tt0) REVERT: A 2220 MET cc_start: 0.6722 (mtm) cc_final: 0.6376 (mtt) REVERT: A 2227 LYS cc_start: 0.5974 (tptt) cc_final: 0.5692 (tppp) REVERT: A 2239 LYS cc_start: 0.6373 (tmmt) cc_final: 0.5842 (ttpt) REVERT: A 2243 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6053 (pt0) REVERT: A 2292 CYS cc_start: 0.6678 (OUTLIER) cc_final: 0.5786 (p) REVERT: A 2356 MET cc_start: 0.6164 (mtm) cc_final: 0.5806 (mtp) REVERT: A 2357 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6271 (mp0) REVERT: A 2369 LYS cc_start: 0.7842 (mttt) cc_final: 0.6604 (mmpt) REVERT: A 2379 MET cc_start: 0.7253 (tpp) cc_final: 0.6930 (tpt) REVERT: A 2427 ARG cc_start: 0.6766 (tpt90) cc_final: 0.6366 (tpm-80) REVERT: A 2430 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5643 (tt0) REVERT: A 2447 LYS cc_start: 0.7643 (mmpt) cc_final: 0.7293 (mmpt) REVERT: A 2450 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7231 (tt0) REVERT: A 2504 ASP cc_start: 0.5971 (m-30) cc_final: 0.5394 (m-30) REVERT: A 2522 ARG cc_start: 0.5783 (tmt170) cc_final: 0.5535 (ttm-80) REVERT: A 2551 GLU cc_start: 0.8169 (tt0) cc_final: 0.7690 (tt0) REVERT: A 2795 GLN cc_start: 0.6473 (tm-30) cc_final: 0.6092 (tp40) REVERT: A 2818 LYS cc_start: 0.7454 (tttt) cc_final: 0.6731 (tttm) REVERT: A 2864 GLN cc_start: 0.7075 (mm-40) cc_final: 0.5889 (tm-30) REVERT: A 2935 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6499 (mm-30) REVERT: A 3007 GLU cc_start: 0.7381 (mp0) cc_final: 0.6379 (mm-30) REVERT: A 3067 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5789 (tttp) REVERT: A 3090 TYR cc_start: 0.7429 (m-80) cc_final: 0.6520 (m-80) REVERT: A 3140 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6858 (mt-10) REVERT: A 3158 LYS cc_start: 0.6696 (mtpp) cc_final: 0.6425 (mtpt) REVERT: A 3173 MET cc_start: 0.6975 (mmm) cc_final: 0.6686 (mpp) REVERT: A 3237 SER cc_start: 0.7556 (t) cc_final: 0.7325 (m) REVERT: A 3238 MET cc_start: 0.7855 (mtm) cc_final: 0.7272 (mtp) REVERT: A 3284 SER cc_start: 0.7486 (p) cc_final: 0.7207 (p) REVERT: A 3287 ARG cc_start: 0.6670 (ptm160) cc_final: 0.6164 (ptm-80) REVERT: A 3289 ARG cc_start: 0.6865 (mpt90) cc_final: 0.6241 (mpt-90) REVERT: A 3327 ASN cc_start: 0.5773 (m-40) cc_final: 0.5236 (m110) REVERT: A 3387 GLU cc_start: 0.6296 (tp30) cc_final: 0.5773 (tt0) REVERT: A 3520 GLU cc_start: 0.4949 (pt0) cc_final: 0.4367 (tp30) REVERT: A 3529 ILE cc_start: 0.6697 (tp) cc_final: 0.6369 (tp) REVERT: A 3718 ARG cc_start: 0.5852 (mpp80) cc_final: 0.5424 (mpp80) REVERT: A 3734 ARG cc_start: 0.6162 (tpp80) cc_final: 0.5258 (tpp-160) REVERT: A 3772 ASN cc_start: 0.6912 (p0) cc_final: 0.6327 (p0) REVERT: A 3838 GLU cc_start: 0.5101 (tm-30) cc_final: 0.4763 (tm-30) REVERT: A 3841 ASP cc_start: 0.5967 (t70) cc_final: 0.5660 (t70) REVERT: A 3863 ASN cc_start: 0.6168 (p0) cc_final: 0.5941 (p0) REVERT: A 3869 THR cc_start: 0.6426 (m) cc_final: 0.6178 (m) REVERT: A 3932 MET cc_start: 0.7630 (mmm) cc_final: 0.7124 (mmm) REVERT: A 4089 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.5993 (pt) REVERT: A 4098 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6553 (mp) REVERT: A 4108 MET cc_start: 0.7677 (ttm) cc_final: 0.7375 (mtt) REVERT: B 78 SER cc_start: 0.7922 (m) cc_final: 0.7713 (m) REVERT: B 107 GLU cc_start: 0.6945 (pt0) cc_final: 0.6309 (mt-10) REVERT: B 130 ARG cc_start: 0.5693 (mtp180) cc_final: 0.5396 (mtp85) REVERT: B 160 LYS cc_start: 0.7498 (tppp) cc_final: 0.6886 (tmtt) REVERT: B 161 MET cc_start: 0.8545 (mtm) cc_final: 0.8175 (mtt) REVERT: B 165 ARG cc_start: 0.7029 (ttp-110) cc_final: 0.6212 (mtp85) REVERT: B 192 ASP cc_start: 0.5594 (t70) cc_final: 0.5216 (t70) REVERT: B 281 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7256 (pp) REVERT: B 294 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6141 (mt-10) REVERT: B 317 LYS cc_start: 0.6015 (mttt) cc_final: 0.5373 (mmmt) REVERT: B 333 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 335 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6548 (tp30) REVERT: B 361 TYR cc_start: 0.6989 (t80) cc_final: 0.6540 (t80) REVERT: B 393 GLU cc_start: 0.5942 (mp0) cc_final: 0.5229 (tt0) REVERT: B 409 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.5737 (t80) REVERT: B 443 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5600 (mtmt) REVERT: C 7 LYS cc_start: 0.6477 (mtpp) cc_final: 0.5948 (mtpm) REVERT: C 20 MET cc_start: 0.3480 (OUTLIER) cc_final: 0.1972 (tpp) REVERT: C 80 HIS cc_start: 0.5142 (t-90) cc_final: 0.4860 (t-90) REVERT: C 210 MET cc_start: 0.5905 (ppp) cc_final: 0.5105 (tpt) REVERT: C 233 LYS cc_start: 0.4019 (mttt) cc_final: 0.3656 (mtpp) REVERT: C 287 GLU cc_start: 0.7279 (mp0) cc_final: 0.6992 (mm-30) REVERT: C 288 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.6006 (m-30) REVERT: C 289 ILE cc_start: 0.6090 (pt) cc_final: 0.5001 (OUTLIER) REVERT: C 304 GLU cc_start: 0.7340 (tt0) cc_final: 0.6913 (tt0) REVERT: C 311 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6888 (tt) REVERT: C 315 ARG cc_start: 0.6870 (tpp-160) cc_final: 0.6277 (tpp80) REVERT: C 332 LYS cc_start: 0.7252 (ptmt) cc_final: 0.6780 (ptmm) REVERT: C 336 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6218 (pp20) REVERT: C 343 LEU cc_start: 0.8345 (mt) cc_final: 0.8013 (mp) REVERT: C 371 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6164 (pp20) REVERT: C 427 MET cc_start: 0.7536 (ppp) cc_final: 0.6900 (pp-130) REVERT: C 481 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6486 (mptm) REVERT: C 482 ILE cc_start: 0.6605 (pt) cc_final: 0.6254 (pt) outliers start: 137 outliers final: 87 residues processed: 740 average time/residue: 1.5543 time to fit residues: 1416.7232 Evaluate side-chains 761 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 650 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1057 LYS Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1712 ARG Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2292 CYS Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2566 THR Chi-restraints excluded: chain A residue 2780 LEU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2820 MET Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3044 MET Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3242 MET Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3496 ILE Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 287 optimal weight: 0.8980 chunk 462 optimal weight: 0.8980 chunk 282 optimal weight: 0.9980 chunk 219 optimal weight: 0.0000 chunk 321 optimal weight: 5.9990 chunk 485 optimal weight: 1.9990 chunk 446 optimal weight: 2.9990 chunk 386 optimal weight: 0.0060 chunk 40 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 533 HIS A 720 GLN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2380 ASN ** A3296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN A3339 ASN A3516 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN C 246 HIS C 411 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40414 Z= 0.216 Angle : 0.685 14.561 54841 Z= 0.339 Chirality : 0.042 0.301 6243 Planarity : 0.005 0.065 6791 Dihedral : 12.136 171.506 5770 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.86 % Allowed : 21.69 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4795 helix: 0.62 (0.10), residues: 2829 sheet: -0.53 (0.37), residues: 204 loop : -2.64 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 645 HIS 0.016 0.001 HIS C 246 PHE 0.027 0.002 PHE A1089 TYR 0.034 0.002 TYR A3442 ARG 0.015 0.001 ARG A3159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 657 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7040 (mm) REVERT: A 41 GLU cc_start: 0.5810 (tt0) cc_final: 0.4943 (tp30) REVERT: A 80 GLU cc_start: 0.6334 (mp0) cc_final: 0.5986 (mp0) REVERT: A 143 LEU cc_start: 0.6509 (mt) cc_final: 0.6034 (mt) REVERT: A 146 GLU cc_start: 0.6191 (tp30) cc_final: 0.5924 (mm-30) REVERT: A 172 GLU cc_start: 0.7742 (tt0) cc_final: 0.6644 (tm-30) REVERT: A 190 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 191 ASN cc_start: 0.7880 (m-40) cc_final: 0.7521 (m110) REVERT: A 243 GLN cc_start: 0.6432 (tp40) cc_final: 0.5624 (mp10) REVERT: A 263 LYS cc_start: 0.7162 (mptt) cc_final: 0.6551 (mppt) REVERT: A 326 MET cc_start: 0.6045 (mtp) cc_final: 0.5499 (mtm) REVERT: A 329 LYS cc_start: 0.6831 (mtmp) cc_final: 0.6533 (mtmm) REVERT: A 332 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6109 (tp30) REVERT: A 335 LYS cc_start: 0.7165 (mtpm) cc_final: 0.6725 (mtpt) REVERT: A 338 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6765 (tt) REVERT: A 340 TYR cc_start: 0.6803 (t80) cc_final: 0.6350 (t80) REVERT: A 342 MET cc_start: 0.6522 (mmt) cc_final: 0.5922 (mmt) REVERT: A 373 CYS cc_start: 0.6967 (m) cc_final: 0.6465 (m) REVERT: A 379 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.6032 (mtpm) REVERT: A 380 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5020 (m-30) REVERT: A 395 MET cc_start: 0.6133 (ptm) cc_final: 0.5660 (ptm) REVERT: A 423 TYR cc_start: 0.7343 (m-80) cc_final: 0.6563 (m-80) REVERT: A 442 GLN cc_start: 0.6482 (tp-100) cc_final: 0.6100 (tp-100) REVERT: A 453 MET cc_start: 0.6677 (tpp) cc_final: 0.6274 (tpp) REVERT: A 476 ARG cc_start: 0.6602 (mtp-110) cc_final: 0.6080 (mmm160) REVERT: A 578 LYS cc_start: 0.6866 (ptpt) cc_final: 0.6358 (ptpp) REVERT: A 669 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6825 (mp) REVERT: A 746 ARG cc_start: 0.7135 (ttp-170) cc_final: 0.6763 (ttp-110) REVERT: A 767 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: A 775 GLU cc_start: 0.6696 (tt0) cc_final: 0.5944 (mp0) REVERT: A 781 ASP cc_start: 0.6594 (m-30) cc_final: 0.6135 (m-30) REVERT: A 783 HIS cc_start: 0.6512 (m-70) cc_final: 0.6230 (m-70) REVERT: A 784 VAL cc_start: 0.5742 (m) cc_final: 0.5413 (p) REVERT: A 786 GLN cc_start: 0.7483 (tm-30) cc_final: 0.6796 (tm-30) REVERT: A 823 GLN cc_start: 0.5724 (tt0) cc_final: 0.5456 (tt0) REVERT: A 828 LYS cc_start: 0.6848 (mmmm) cc_final: 0.6423 (mttp) REVERT: A 851 ILE cc_start: 0.7189 (mm) cc_final: 0.6984 (mm) REVERT: A 857 GLN cc_start: 0.7011 (mt0) cc_final: 0.6108 (mm110) REVERT: A 879 MET cc_start: 0.7383 (ttm) cc_final: 0.7172 (ttm) REVERT: A 881 LYS cc_start: 0.6553 (mttp) cc_final: 0.5880 (mmmt) REVERT: A 889 GLU cc_start: 0.6378 (tm-30) cc_final: 0.5734 (tp30) REVERT: A 900 GLU cc_start: 0.4702 (tm-30) cc_final: 0.4395 (tm-30) REVERT: A 944 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5893 (mttp) REVERT: A 983 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6458 (mt) REVERT: A 989 MET cc_start: 0.5944 (mmt) cc_final: 0.5562 (mmm) REVERT: A 990 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.6042 (pm20) REVERT: A 1014 LEU cc_start: 0.5007 (mt) cc_final: 0.4775 (mt) REVERT: A 1015 ASP cc_start: 0.6136 (m-30) cc_final: 0.5788 (m-30) REVERT: A 1061 LYS cc_start: 0.6883 (mtpm) cc_final: 0.6513 (mtpp) REVERT: A 1076 LEU cc_start: 0.6129 (tp) cc_final: 0.5924 (tm) REVERT: A 1083 ASN cc_start: 0.6149 (t0) cc_final: 0.5667 (m-40) REVERT: A 1125 GLN cc_start: 0.6796 (tp40) cc_final: 0.5928 (tp-100) REVERT: A 1129 ASP cc_start: 0.5365 (t70) cc_final: 0.4282 (m-30) REVERT: A 1509 GLN cc_start: 0.6054 (tt0) cc_final: 0.5148 (tp-100) REVERT: A 1576 ASP cc_start: 0.5965 (p0) cc_final: 0.5565 (m-30) REVERT: A 1607 GLU cc_start: 0.6413 (mm-30) cc_final: 0.6088 (mm-30) REVERT: A 1627 LYS cc_start: 0.7241 (mmpt) cc_final: 0.6749 (mtmt) REVERT: A 1735 ARG cc_start: 0.5629 (mtm-85) cc_final: 0.5333 (ptp-170) REVERT: A 1761 LEU cc_start: 0.5955 (mt) cc_final: 0.5690 (mp) REVERT: A 1762 MET cc_start: 0.4662 (mmp) cc_final: 0.4313 (mmp) REVERT: A 1775 GLU cc_start: 0.6144 (tt0) cc_final: 0.5540 (mt-10) REVERT: A 1784 ARG cc_start: 0.5075 (ttp-110) cc_final: 0.4118 (mtm110) REVERT: A 1795 VAL cc_start: 0.6710 (t) cc_final: 0.6246 (t) REVERT: A 1799 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5333 (mt-10) REVERT: A 1849 ASP cc_start: 0.5969 (t0) cc_final: 0.4879 (m-30) REVERT: A 1971 PRO cc_start: 0.4015 (Cg_endo) cc_final: 0.3798 (Cg_exo) REVERT: A 2042 GLN cc_start: 0.6200 (OUTLIER) cc_final: 0.5134 (tm-30) REVERT: A 2085 MET cc_start: 0.5565 (pmm) cc_final: 0.5236 (pmm) REVERT: A 2091 HIS cc_start: 0.6193 (t-90) cc_final: 0.5974 (t70) REVERT: A 2127 LYS cc_start: 0.6479 (mptt) cc_final: 0.5984 (mptt) REVERT: A 2163 HIS cc_start: 0.6876 (m90) cc_final: 0.6159 (m-70) REVERT: A 2170 GLN cc_start: 0.6243 (tt0) cc_final: 0.5962 (tt0) REVERT: A 2220 MET cc_start: 0.6849 (mtm) cc_final: 0.6476 (mtt) REVERT: A 2239 LYS cc_start: 0.6441 (tmmt) cc_final: 0.5899 (ttpt) REVERT: A 2243 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6038 (pt0) REVERT: A 2292 CYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5775 (p) REVERT: A 2341 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6721 (mm) REVERT: A 2356 MET cc_start: 0.6110 (mtm) cc_final: 0.5785 (mtp) REVERT: A 2357 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6273 (mp0) REVERT: A 2362 VAL cc_start: 0.7646 (t) cc_final: 0.7297 (m) REVERT: A 2369 LYS cc_start: 0.7829 (mttt) cc_final: 0.6573 (mmpt) REVERT: A 2379 MET cc_start: 0.7198 (tpp) cc_final: 0.6684 (tpt) REVERT: A 2419 ASP cc_start: 0.6677 (t0) cc_final: 0.6220 (m-30) REVERT: A 2427 ARG cc_start: 0.6731 (tpt90) cc_final: 0.6111 (tpm-80) REVERT: A 2430 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5664 (tt0) REVERT: A 2434 VAL cc_start: 0.6971 (t) cc_final: 0.6712 (p) REVERT: A 2447 LYS cc_start: 0.7791 (mmpt) cc_final: 0.7341 (mmpt) REVERT: A 2450 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7225 (tt0) REVERT: A 2504 ASP cc_start: 0.5912 (m-30) cc_final: 0.5292 (m-30) REVERT: A 2522 ARG cc_start: 0.5512 (tmt170) cc_final: 0.5236 (ttm-80) REVERT: A 2537 ASP cc_start: 0.6051 (m-30) cc_final: 0.5699 (m-30) REVERT: A 2551 GLU cc_start: 0.7988 (tt0) cc_final: 0.7578 (tt0) REVERT: A 2795 GLN cc_start: 0.6502 (tm-30) cc_final: 0.6167 (tp40) REVERT: A 2818 LYS cc_start: 0.7432 (tttt) cc_final: 0.6710 (tttm) REVERT: A 2864 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6003 (tm-30) REVERT: A 2935 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6545 (mm-30) REVERT: A 2980 ASP cc_start: 0.5257 (OUTLIER) cc_final: 0.4596 (t0) REVERT: A 3007 GLU cc_start: 0.7237 (mp0) cc_final: 0.6314 (mm-30) REVERT: A 3067 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6076 (tttp) REVERT: A 3090 TYR cc_start: 0.7519 (m-80) cc_final: 0.6466 (m-80) REVERT: A 3140 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6327 (mt-10) REVERT: A 3158 LYS cc_start: 0.6701 (mtpp) cc_final: 0.6408 (mtpt) REVERT: A 3159 ARG cc_start: 0.5718 (ttp-110) cc_final: 0.5410 (ttp-110) REVERT: A 3172 LYS cc_start: 0.7599 (ttmm) cc_final: 0.7126 (ttmt) REVERT: A 3173 MET cc_start: 0.7045 (mmm) cc_final: 0.6625 (mpp) REVERT: A 3287 ARG cc_start: 0.6630 (ptm160) cc_final: 0.6092 (ptm-80) REVERT: A 3289 ARG cc_start: 0.6795 (mpt90) cc_final: 0.6160 (mpt-90) REVERT: A 3327 ASN cc_start: 0.5781 (m-40) cc_final: 0.5419 (m110) REVERT: A 3387 GLU cc_start: 0.6281 (tp30) cc_final: 0.5149 (tp30) REVERT: A 3520 GLU cc_start: 0.5105 (pt0) cc_final: 0.4496 (tp30) REVERT: A 3529 ILE cc_start: 0.6572 (tp) cc_final: 0.6233 (tp) REVERT: A 3718 ARG cc_start: 0.5832 (mpp80) cc_final: 0.5413 (mpp80) REVERT: A 3734 ARG cc_start: 0.6159 (tpp80) cc_final: 0.5274 (tpp-160) REVERT: A 3772 ASN cc_start: 0.6877 (p0) cc_final: 0.6315 (p0) REVERT: A 3796 MET cc_start: 0.8110 (mmp) cc_final: 0.7330 (mmm) REVERT: A 3831 ASP cc_start: 0.6795 (t0) cc_final: 0.6421 (t0) REVERT: A 3838 GLU cc_start: 0.5014 (tm-30) cc_final: 0.4621 (tm-30) REVERT: A 3841 ASP cc_start: 0.5901 (t70) cc_final: 0.5630 (t70) REVERT: A 3863 ASN cc_start: 0.6312 (p0) cc_final: 0.6092 (p0) REVERT: A 3869 THR cc_start: 0.6383 (m) cc_final: 0.6145 (m) REVERT: A 3877 LYS cc_start: 0.7198 (mtmm) cc_final: 0.6735 (tptp) REVERT: A 3932 MET cc_start: 0.7630 (mmm) cc_final: 0.7309 (mmm) REVERT: A 4089 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6224 (pt) REVERT: A 4108 MET cc_start: 0.7594 (ttm) cc_final: 0.7319 (mtt) REVERT: B 78 SER cc_start: 0.7946 (m) cc_final: 0.7731 (m) REVERT: B 130 ARG cc_start: 0.5713 (mtp180) cc_final: 0.5428 (mtp85) REVERT: B 160 LYS cc_start: 0.7522 (tppp) cc_final: 0.6841 (tmtt) REVERT: B 161 MET cc_start: 0.8418 (mtm) cc_final: 0.8001 (mtt) REVERT: B 165 ARG cc_start: 0.6981 (ttp-110) cc_final: 0.6217 (mtp85) REVERT: B 192 ASP cc_start: 0.5493 (t70) cc_final: 0.5148 (t70) REVERT: B 281 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7145 (pp) REVERT: B 294 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6290 (mt-10) REVERT: B 317 LYS cc_start: 0.6002 (mttt) cc_final: 0.5366 (mmmt) REVERT: B 333 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6645 (mt-10) REVERT: B 335 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6515 (tp30) REVERT: B 393 GLU cc_start: 0.5999 (mp0) cc_final: 0.5278 (tt0) REVERT: B 409 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.5666 (t80) REVERT: B 443 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5533 (mtmt) REVERT: C 7 LYS cc_start: 0.6521 (mtpp) cc_final: 0.5911 (mtpm) REVERT: C 20 MET cc_start: 0.3509 (OUTLIER) cc_final: 0.1970 (tpp) REVERT: C 80 HIS cc_start: 0.5161 (t-90) cc_final: 0.4853 (t-90) REVERT: C 210 MET cc_start: 0.5887 (ppp) cc_final: 0.5088 (tpt) REVERT: C 286 LYS cc_start: 0.6686 (ttpt) cc_final: 0.6221 (ttpp) REVERT: C 287 GLU cc_start: 0.7279 (mp0) cc_final: 0.6725 (mp0) REVERT: C 288 ASP cc_start: 0.6343 (OUTLIER) cc_final: 0.6058 (m-30) REVERT: C 289 ILE cc_start: 0.5996 (pt) cc_final: 0.4889 (OUTLIER) REVERT: C 311 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6729 (tt) REVERT: C 315 ARG cc_start: 0.6758 (tpp-160) cc_final: 0.6191 (tpp80) REVERT: C 336 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6068 (pp20) REVERT: C 343 LEU cc_start: 0.8318 (mt) cc_final: 0.7991 (mp) REVERT: C 371 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6206 (pp20) REVERT: C 389 MET cc_start: 0.7149 (tpt) cc_final: 0.6490 (mmp) REVERT: C 427 MET cc_start: 0.7586 (ppp) cc_final: 0.6860 (pp-130) REVERT: C 482 ILE cc_start: 0.6588 (pt) cc_final: 0.6258 (pt) REVERT: C 552 GLU cc_start: 0.6926 (pt0) cc_final: 0.6515 (pp20) outliers start: 118 outliers final: 77 residues processed: 724 average time/residue: 1.5188 time to fit residues: 1353.6652 Evaluate side-chains 742 residues out of total 4334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 643 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1057 LYS Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1712 ARG Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2292 CYS Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2566 THR Chi-restraints excluded: chain A residue 2780 LEU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2820 MET Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 2998 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3044 MET Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3242 MET Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 306 optimal weight: 0.8980 chunk 411 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 356 optimal weight: 0.9990 chunk 57 optimal weight: 0.0000 chunk 107 optimal weight: 0.0370 chunk 386 optimal weight: 0.6980 chunk 161 optimal weight: 0.0170 chunk 397 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 0.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 720 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN A3516 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.221742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.194792 restraints weight = 64269.368| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.89 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40414 Z= 0.192 Angle : 0.661 12.143 54841 Z= 0.327 Chirality : 0.041 0.296 6243 Planarity : 0.005 0.064 6791 Dihedral : 12.009 172.068 5770 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.31 % Allowed : 22.47 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4795 helix: 0.80 (0.10), residues: 2811 sheet: -0.45 (0.38), residues: 206 loop : -2.59 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2479 HIS 0.012 0.001 HIS A1367 PHE 0.026 0.001 PHE A1089 TYR 0.029 0.001 TYR A3442 ARG 0.014 0.000 ARG A3159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19120.91 seconds wall clock time: 344 minutes 8.68 seconds (20648.68 seconds total)